Clone id Clone ID of EST sequence of Adiantum capillus-veneris. Library Library name Length Number of bases Definition Definition Accession DDBJ accession number Tissue type Name of the tissue from which the sequence is derived Developmental stage Developmental stage Sequence(60) Nucleotide sequence (line break after 60 characters) sequence Nucleotide sequence (without line break) ||Homology search results|| Swiss-Prot (release 56.9) Results of blastx search against Swiss-Prot (release 56.9) UniProt ID of top hit in Swiss-Prot UniProt ID of the hit sequence with the highest score in the blastx search against Swiss-Prot (release 56.9) Definition Accession and definition of the hit sequence with the highest score in the blastx search against Swiss-Prot (release 56.9). Link to Uniprot is provided in TogoDB. Align length The alignment length between the query and the hit sequence with the highest score in the blastx search against Swiss-Prot (release 56.9). Score (bit) Score (bit) of the alignment between the query and the hit sequence with the highest score in the blastx search against Swiss-Prot (release 56.9). E-value E-value of the alignment between the query and the hit sequence with the highest score in the blastx search against Swiss-Prot (release 56.9). Report Results of blastx search against the UniProtKB/Swiss-Prot (release 56.9) database. TrEMBL (release 39.9) Results of blastx search against TrEMBL (release 39.9) UniProt ID of top hit in TrEMBL UniProt ID of the hit sequence with the highest score in the blastx search against TrEMBL (release 39.9). Definition Accession and definition of the hit sequence with the highest score in the blastx search against TrEMBL (release 39.9). Link to Uniprot is provided in TogoDB. Align length The alignment length between the query and the hit sequence with the highest score in the blastx search against TrEMBL (release 39.9). Score (bit) Score (bit) of the alignment between the query and the hit sequence with the highest score in the blastx search against TrEMBL (release 39.9). E-value E-value of the alignment between the query and the hit sequence with the highest score in the blastx search against TrEMBL (release 39.9). Report Results of blastx search against the UniProtKB/TrEMBL (release 39.9) database.

Query Clone ID of Adiantum capillus-veneris EST sequence used for query BlastX Hits Accession and definition of the hit sequence in the blastx search against the UniProtKB/Swiss-Prot (release 56.9) database. Link to Uniprot is provided in TogoDB. Align Length The alignment length between the above hit sequence and an Adiantum capillus-veneris EST sequence Bit score Score (bit) of the alignment between the above hit sequence and an Adiantum capillus-veneris EST sequence E-value E-value of the alignment between the above hit sequence and an Adiantum capillus-veneris EST sequence Report Results of blastx search against the UniProtKB/Swiss-Prot (release 56.9) database. UniProt ID UniProt ID of the above hit sequence

Query Clone ID of Adiantum capillus-veneris EST sequence subjected to the blastX search BlastX Hits Accession and definition of the hit sequence in the blastx search against the UniProtKB/TrEMBL (release 39.9) database. Link to Uniprot is provided in TogoDB. Align Length The alignment length between the above hit sequence and an Adiantum capillus-veneris EST sequence Bit score Score (bit) of the alignment between the above hit sequence and an Adiantum capillus-veneris EST sequence E-value E-value of the alignment between the above hit sequence and an Adiantum capillus-veneris EST sequence Report Results of blastx search against the UniProtKB/TrEMBL (release 39.9) database UniProt ID UniProt ID of the above hit sequence

Contig ID ID of contig sequence of Adiantum capillus-veneris Length Length of the contig sequence of Adiantum capillus-veneris Number of clones The number of EST clones constituting the contig sequence of Adiantum capillus-veneris Definition Definition Link to clone list In the TogoDB edition, link to a list of EST clones constituting the contig sequence of Adiantum capillus-veneris is provided. It is blank in the downloaded file. Clone ID ID of the EST clone constituting the contig sequence of Adiantum capillus-veneris with link to the AcEST clone information Sequence Nucleotide sequence

Name Name of Adiantum capillus-veneris EST library About Adiantum capillus-veneris EST library creation information References References of creation of Adiantum capillus-veneris EST library

PRJID BioProject ID of the project where data is obtained AEID ArrayExpress ID of data (Link to ArrayExpress in simple search) GSE GEO SeriesID of data (Link to GEO in simple search) Description Data description Date Data submission date ArrayType ArrayType ArrayGroup ArrayType group Technology Experiment technology Instrument Instrument name or ID of BioProject entry where instument information is described NGSGroup Instrument group when NGS is used Organisms Organisms Rep_organism Representative of Organisms

Entry URI Entry URI Image Mutant image Entry name Entry name Original data name Name in the original database Observed phenotype Observed phenotype Phenotype URI Phenotype URI Modified gene Modified gene

Entry URI Entry URI Entry name Entry name Entity in PO Entity (defined in PO) Quality in PATO Quality (defined in PATO) Num of observation data The number of entries where the phenotype is used in "Observation of Arabidopsis phenotype"

Entry URI Entry URI Entry name Entry name Reference Curated reference Reference URI Reference URI Pheno abnormality Pheno abnormality Abnormality URI Abnormality URI Muteted gene Muteted gene

Entry URI Entry URI Entry name Entry name Experimental condition Experimental condition Condition URI Condition URI Quality in PATO Quality (defined in PATO) In organ named In organ named In period of In period of In response to organism In response to organism In situation of In situation of After After Under influence of Under influence of During process named During process named Exhibited by Exhibited by For quantity of For quantity of For state of For state of For trait of For trait of Num of phenotype gene The number of entries where the abnormality is used in "Phenotype-gene"

Entry URI Entry URI Entry name Entry name Description Description In environment of In environment of In presence of In presence of In absense of In absense of Num of phenotype abnormality The number of entries where the condition is used in "Phenotype abnormality"

Entry URI Entry URI Entry name Entry name Title Title Authors Authors Abstract Abstract Pubmed ID Pubmed ID Journal Journal Volume Volume Issue Issue Pages Pages Publication date Publication date Num of phenotype gene The number of entries where the reference is used in "Phenotype-gene"

Locus ID Specific locus ID for this database UniGene ID UniGene ID Species Species name Chr. No. Chromosome No. Strand Strand Matched genome Definition of the genome sequence matching this locus Matched genome (GI) Genbank ID of the genome sequence matching this locus Matched genome (RefSeq) RefSeq ID of the genome sequence matching this locus Gene name Gene name Left The left position of this locus onto genome Right The right position of this locus onto genome GO Gene Ontology Variants Number of splicing variants Splicing type Splicing type (ex. cassette)

cDNA ID Specific cDNA ID for this database Locus ID Specific locus ID for this database Species Species name Chr. No. Chromosome No. Strand Strand Gene name Gene name UniGene ID UniGene ID cDNA UniGene ID UniGene ID of this cDNA Genbank accession Genbank accession number GI Genbank ID CDS left The left position of coding region onto this cDNA CDS right The right position of coding region onto this cDNA Splicing pattern Splicing pattern (gene model) cDNA sequence length cDNA sequence length DOU start Premature (pseudo) start codon (true) or not (false) DOU end Premature (pseudo) stop codon (true) or not (false) NMD Nonsense-mediated mRNA Decay (NMD) might happen (true) or not (false) Number of exons Number of exons in this variant Number of splicing regions Number of alternative splicing/transcriptional initiation regionss

Exon ID Specific exon ID for this database Species Species name Locus ID Specific locus ID for this database cDNA ID Specific cDNA ID for this database Left in cDNA The left position of exon onto cDNA Right in cDNA The right position of exon onto cDNA Left in genome The left position of exon onto genome Right in genome The right position of exon onto genome

ID ID for splicing pattern Species Species name Locus ID Specific locus ID for this database Region Splicing Region number in this locus Splicing pattern Splicing pattern number in this locus cDNA ID Specific cDNA ID for this database Splicing left The left position of splicing region onto genome Splicing right The right position of splicing region onto genome Splicing pattern Splicing pattern represented into bit array. "1" means splicing region. Splicing type Splicing type (ex. cassette) NAGNAG NAGNAG (6bp acceptor site) or not

ID ID of the subject (There are one to six technological subjects in a project.) Project ID ID of the project Subject Subject in the project Project Theme Theme of the project Principal Investigator Principal Investigator of the project Affiliation Affiliation of the project Backgrounds Backgrounds of the subject Highlights Highlights of the subject Outline Outline of the protocol Application Project ID (in TPRP) that carried out using the protocol Article Related paper (In the cases of multiple items, they are arranged in the same order as PubMed ID.) PubMed ID PubMed ID (In the cases of multiple items, they are arranged in the same order as Article.) CSML File Name of the diagram data (CMSL file) (Linked to the diagram data in the Simple Search site.)

Project ID Project ID PDB ID PDB ID in PDBj Protein Name Name of the protein

Project ID Project ID Protocol ID Protocol ID in PREIMS (PRotein Experimental Information Management Sysmtem) Protocol Name Name of the protocol Category Category of the protocol Author Author of the protocol

concept id ID of the corresponding FMA (Foundational Model of Anatomy). representation id ID of the corresponding 3D representation. en English name. Basically, a preferred name of FMA is assigned.

concept id ID of the corresponding FMA (Foundational Model of Anatomy). representation id ID of the corresponding 3D representation. en English name. Basically, a preferred name of FMA is assigned.

parent id Concept ID of parent organ parent name English name of parent organ child id Concept ID of an organ that is included in the parent organ child name English name of an organ that included in the parent organ

parent id Concept ID of parent organ parent name English name of parent organ child id Concept ID of an organ that is included in the parent organ child name English name of an organ that included in the parent organ

concept id Concept ID of COMPOUND organ name Name of COMPOUND organ element file id Polygon mesh file ID of ELEMENT constituting the COMPOUND organ

concept id Concept ID of COMPOUND organ name Name of COMPOUND organ element file id Polygon mesh file ID of ELEMENT constituting the COMPOUND organ

Clone ID Clone ID, and name in the SGD. Link to SGD Link to SGD (Saccharomyces Genome Database, http://www.yeastgenome.org/) based on the clone ID of the cDNAs mapped to the genome. The link is found in the TogoDB edition, and only Clone ID is found in the archive file. Link to dbEST Link to NCBI's dbEST based on accession of the GenBank for the cDNAs possessing genuine 5'-end. The link is found in the TogoDB edition, and the archive file has accession only. Link to UCSC Genome Browser Link to the UCSC Genome Browser based on accession of the GenBank for the cDNAs possessing genuine 5'-end. The link is found in the TogoDB edition, and the archive file has accession only. Sequence 5'-end sequence data of budding yeast full-length cDNA clones. FASTA format. Quality Phred's quality score

Project ID Project ID Link Links to "Sample" and "Measured Data" obtained in this project (Only simple search) Submitter Name Submitter name Submitter Affiliation Submitter affiliation Submitter Department Submitter department Submetter City Submetter city Submetter Country Submetter country Corresponding Author Name Corresponding author name Corresponding Author Affiliation Corresponding author affiliation Corresponding Author Department Corresponding author department Corresponding Author City Corresponding author city Corresponding Author Country Corresponding author country Release Date Data release date Title Article title Publication Article ID (DOI) Grant Grant to this project

Sample ID Sample ID Link Links to "Measured Data" obtained in this sample (Only simple search) Project ID ID of sampling project Sample Type 1 Sample type Sample Type 2 Sample type Sample Type 3 Sample type Sample Type 4 Sample type Sample Type 5 Sample type Taxonomy ID Taxonomy ID for biotic sample es-BANK ID ID of Environmental Specimen Bank (es-BANK) Sample Name Sample name Scientific Name Scientific name Common Name Common name Sampling Time Sampling time Weather Weather at sampling Region Region Country Country Area Area Latitude From Latitude from Latitude To Latitude to Longitude From Longitude from Longitude To Longitude to Sex Sex for biotic sample Tissue Organ Organ for biotic sample Tissue Lipid Lipid weight for biotic sample Tissue Moist Moist weight for biotic sample Weight Weight Weight Unit Weight unit Length Length Length Unit Length unit Length Type Length type Growth Stage Growth stage for biotic sample Age Age for biotic sample Disease Disease for biotic sample Temperature Temperature Water Temperature Water temperature pH pH for water sample DO Dissolved oxygen for water sample EC Electrical conductivity for water sample Salinity Salinity for water sample SS Suspended solids for water sample Water Depth Water depth Transparency Transparency for water sample Water Color Color for water sample Sediment Temperature Temperature for sediment sample Sediment Depth Water depth for sediment sample Sediment Appearance Appearance for sediment sample Sediment Color Color for sediment sample Sediment Surface Color Surface color for sediment sample Sediment Odor Odor for sediment sample Sediment Impurities Impurities for sediment sample Sediment Moisture Onsite Analysis Moisture weight for sediment sample Ignition Loss Onsite Analysis Ignition loss for sediment sample Soil Depth Depth for soil sample Flow Rate Flow rate for air sample Mean PM10 Mean amount of PM10 for air sample Mean Total Suspended Particles Mean total suspended particles for air sample Humidity Humidity for air sample Wind Direction Wind direction for air sample Wind Speed MS Wind speed (m/sec) for air sample Amount of Collected Air Amount of collected Air

Chemical ID Chemical ID Chemical Name Chemical Name IUPAC IUPAC Synonyms Synonyms PubChem PubChem ID CAS CAS Number Link Links to "Measured Data" that contains this chemical (Only simple search)

Measured ID Measured ID Project ID ID of measuring project Sample ID ID of measured sample Instrument Group Instrument group Instrument Instrument name Method Extraction Extraction method Method Cleanup Cleanup method Derivatization Derivatization method Recovery Correction Recovery correction method LOD Limit Of Detection of instrument Repeatability Repeatability Standard Standard instrument for analysis Chemical ID ID of detected chemical Measured Value Measured value Alternative Value Alternative Value Unit Measure unit

Experimental ID Experimental ID (SRX, ERX, DRX) Genome assembly Genome assembly Antigen class Antigen class Antigen Antigen Cell type class Cell type class Cell type Cell type Cell type description Cell type description Processing logs Processing logs (# of reads, % mapped, % duplicates, # of peaks [q < 1E-05]) Title Title submitted by authors Meta data Meta data submitted by authors BigWig Link to a BigWig-formatted coverage score binary file. Peak-call (BED) (q < 1E-05) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-05. Peak-call (BED) (q < 1E-10) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-10. Peak-call (BED) (q < 1E-20) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-20. Peak-call (BigBed) (q < 1E-05) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-05). Peak-call (BigBed) (q < 1E-10) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-10). Peak-call (BigBed) (q < 1E-20) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-20).

File name File name Genome assembly Genome assembly Antigen class Antigen class Antigen Antigen Cell type class Cell type class Cell type Cell type Threshold Threshold Experimental IDs included Experimental IDs included Peak-call (BED) Link to a BED9 + GFF3 format file concatenated and converted from the BED4-formatted peak-call data files of the experiments in the "Experimental IDs included".

Antigen Antigen Cell type class in Colocalization Cell type class in Colocalization (comma separated) Recorded (+) or not (-) in Target Genes Target gene analysis performed or not (+/-) Genome assembly Genome assembly Target Genes (TSS ±1k) Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 1 kb of each TSS (transcription start site). Target Genes (TSS ±5k) Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 5 kb of each TSS (transcription start site). Target Genes (TSS ±10k) Link to a TSV (Tab-Separeted Values) file that describes the genes bound by the given antigen in the range of ± 10 kb of each TSS (transcription start site). Colocalization (TSV) Link to a TSV (Tab-Separeted Values) file that describes the protein colocalization with the given antigen in the given cell type class. Colocalization (GML) Link to a GML (Graph Modelling Language) file that describes the protein colocalization in the given cell type class.

Genome assembly Genome assembly Antigen class Antigen class Antigen Antigen Number of experiments Number of experiments Experimental IDs included Experimental IDs included

Genome assembly Genome assembly Cell type class Cell type class Cell type Cell type Number of experiments Number of experiments Experimental IDs included Experimental IDs included

Clone ID ID of the clone Library Tissue used for library construction Category Category of affiliation of sequence Cluster ID of cluster to which the clone belongs ACC No. of clone Accession number of the clone in GenBank Length Sequence length of the clone Sequence Sequence

Cluster ID ID of the cluster Description Description of presumed function of the cluster Category Category of affiliation of the cluster Length Consensus sequence length of the cluster Sequence Consensus sequence Source Source clones No. of clones Number of source clones Top Blastx hit (E value &lt; 1e-6) Gene name of top Blastx hit ACC No. Accession number of top Blastx hit E-value E-value of top Blastx hit GO GO annotation

confID ID of this table classID ID including structural change class information index Record Index pdbIDA PDB ID compared protein structure A pdbIDB PDB ID compared protein structure B pdbChainA PDB chain ID compared protein structure A pdbChainB PDB chain ID compared protein structure B confDatafile Link to conformation analysis file (zip) confClass Binding molecular type confName Name of binding molecules dmax Maximum distance between C&alpha; atoms of superimposed protein structures rmsd RMSD of distance between C&alpha; of superimposed protein structures identity Protein sequence identity

confID ID of ConfAll table siteNo Site number in residue number order siteStart1 Dihedral angle number at the start of the site in the structure 1 (numbering starts at the second visible residue) siteStartR1 Residue number at the start of the site in the structure 1 siteEnd1 Dihedral angle number at the end of the site in the structure 1 siteEndR1 Residue number at the end of the site in the structure 1 siteLength1 The longest site length in the structure 1 siteStart2 Dihedral angle number at the start of the site in the structure 2 (numbering starts at the second visible residue) siteStartR2 Residue number at the start of the site in the structure 2 siteEnd2 Dihedral angle number at the end of the site in the structure 2 siteEndR2 Residue number at the end of the site in the structure 2 siteLength2 The longest site length in the structure 2 phiMax Maximum value of &phi;change psiMax Maximum value of &psi;change

confEVID ID of this table pdbIDA PDB ID of compared protein structure A pdbIDB PDB ID of compared protein structure B pdbChainA PDB chain ID of compared protein structure A pdbChainA PDB chain ID of compared protein structure B identity Sequence identity indelSize Number of indels analyzed alignment Sequence alignment indel Analysis of indels

confID ID of this table classID ID of structural change class pdbID PDB ID pdbChain PDB chain ID method Experimental technique used for the structure determination program Refinement program temperature Temperature at experiment resolution Resolution Rfactor R-factor depositDate Deposition date depositDateClass Date format ECnumber EC number SCOPID SCOP ID domainNumber Number of domains complex Type of complex SEQRESLength SEQRES Length ATOMLength ATOM Length REMARK465 Whether REMARK 465 (describing missing residues) is used disorderNumber Number of disorder regions disSumLength Total number of disordered residues maxDisLength Maximum length of disorder region minDisLength Minimum length of disorder region disSeqresPosition Position of disorder regions by SEQRES disAtomPosition Position of disorder regions by ATOM temperatureFactorAve Average of temperature factor temperatureFactorStddev Standard deviation of temperature factor checkOccupy Whether OCCUPANCY less than 1.00 is used modelNumber Whether MODEL NUMBER is used

mKIAA No. Gene number of mouse KIAA Clone name Name of the clone Accession No. Accession number for DDBJ/GenBank/EMBL database Alias Name Gene name Antigen size Size of the antigen Antigen solubility Solubility of the antigen Homolog human clone Clone name for the human homolog Reference protein Reference protein Predicted molecular weight Predicted molecular weight Predicted gene function Predicted gene function (Gene Ontology number) Antigen sequence name Name of the antigen Antigen sequence Amino acids sequence of the antigen Purification tag Status of the purification tag Western blot (adult organs) Results of the Western blot (adult mouse organs) Western blot (cell lines) Results of the Western blot (Cultured cell lines) Infrared Fluorescence scanner (cerebellum) Observation by Infrared Fluorescence scanner (cerebellum) Infrared Fluorescence scanner (forebrain 1) Observation by Infrared Fluorescence scanner (forebrain 1) Infrared Fluorescence scanner (forebrain 2) Observation by Infrared Fluorescence scanner (forebrain 2) Confocal laser scanning microscope (neocortex 1) Observation by Confocal laser scanning microscope (neocortex 1) Confocal laser scanning microscope (neocortex 2) Observation by Confocal laser scanning microscope (neocortex 2) Confocal laser scanning microscope (hippocampus) Observation by Confocal laser scanning microscope (hippocampus) Confocal laser scanning microscope (cerebellum) Observation by Confocal laser scanning microscope (cerebellum) Immunoprecipitation Results of the immunoprecipitation Mascot search results Results of the Mascot search in MS Ectopic expression (phase) Expression of KIAA gene in HEK293 cells (phase) Ectopic expression (fluoro) Expression of KIAA gene in HEK293 cells (fluoro) mKIAA cDNA array analysis Results of mKIAA cDNA array analysis

mKIAA No. Gene number of mouse KIAA Pathway image Image for the signal transduction pathway KeyMolnet file File derived from KeyMolnet software Reference Related research paper

RefSNP ID RefSNP ID (rs number) given by dbSNP. (Linked to dbSNP in Quick Search) Affy/Perlegen ID SNP ID given by Affymetrix or Perlegen Chromosome Chromosome number that each SNP resides Position Chromosomal nucleotide position (NCBI Build 35) of each SNP Alleles Alleles MAF Minor allele frequency Genotypes Genotypes for the 74 CHM samples LD bin Name of LD bin (Linked to LD bin list in Quick Search) tagSNP The flag that indicates whether the SNP is a tagSNP or not. 1: tagSNP 0: non-tagSNP -: SNP not included in LD bin calculation (MAF<0.05) Best tagSNP The flag that indicates whether the SNP is the best tagSNP or not. 1: Best tagSNP 0: non-best tagSNP -: SNP not included in LD bin calculation (MAF<0.05)

RefSNP ID RefSNP ID (rs number) given by dbSNP. (Linked to dbSNP in Quick Search) Affy/Perlegen ID SNP ID given by Affymetrix Chromosome Chromosome number that each SNP resides Position Chromosomal nucleotide position (NCBI Build 36) of each SNP Alleles Alleles MAF Minor allele frequency Genotypes Genotypes for the 87 CHM samples LD bin Name of LD bin (Linked to LD bin list in Quick Search) tagSNP The flag that indicates whether the SNP is a tagSNP or not. 1: tagSNP 0: non-tagSNP -: SNP not included in LD bin calculation (MAF<0.05) Best tagSNP The flag that indicates whether the SNP is the best tagSNP or not. 1: Best tagSNP 0: non-best tagSNP -: SNP not included in LD bin calculation (MAF<0.05)

LD bin Name of LD bin Chromosome Chromosome number each LD bin resides (Chr1 - Chr22, ChrX) Position Start Start position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35) Position End End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35) SNPs Count Number of SNPs in LD bin tagSNPs Count Number of tagSNPs in LD bin Best tagSNP tagSNP that showed the highest mean r2, given by RefSNP ID (rs number)

LD bin Name of LD bin Chromosome Chromosome number each LD bin resides (Chr1 - Chr22, ChrX) Position Start Start position of LD bin (nucleotide position in each chromosome, according to NCBI Build 36) Position End End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 36) SNPs Count Number of SNPs in LD bin tagSNPs Count Number of tagSNPs in LD bin Best tagSNP tagSNP that showed the highest mean r2, given by RefSNP ID (rs number) (Link to dbSNP available in quick search)

rs RefSNP accession ID (rs number) chr Chromosome number that the SNP resides (1 - 22, X) pos Nucleotide position on chromosome that the SNP resides allele1 allele 1 allele2 allele 2 gtype genotypes of 74 samples of CHMs

chr Chromosome number (1-22,X) sample Sample (CHM) name rs RefSNP accession ID (rs number) pos Nucleotide position on chromosome allele1 allele 1 allele2 allele 2 gtype genotypes of 87 CHM samples ss Unique ID, given by Affymetrix

seqname Chromosome that the SNP resides (e.g. Chr1) source name of dataset (e.g. CHM_2R80M5Z) feature description of data. SNP information or LD bin boundary(e.g. LD_BIN, LD_BIN_BOUNDARIES) start Chromosomal position of SNP or start position of bin (NCBI Build 35) end Chromosomal position of SNP or end position of bin score LD_BIN line: 2 for Best tagSNP, and 1 for tagSNP, and 0 for other SNP. LD_BIN_BOUNDARIES line: always "." strand always "+" frame always "," attributes This column contains the following items. - ld_bin: LD bin name - RSID: RefSNP ID (rs number) - tagging: flag that indicates tagSNP - besttag: flag that indicates Best tagSNP - SNPID: unique ID given by Affymetrix (e.g. ld_bin 2R80M5Z_10_1 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)

seqname Chromosome that the SNP resides (e.g. Chr1) source name of dataset (e.g. CHM_3R80M5Z) feature description of data. SNP information or LD bin boundary (e.g. LD_BIN, LD_BIN_BOUNDARIES) start Chromosomal position of SNP or start position of bin (NCBI Build 36) end Chromosomal position of SNP or end position of bin score LD_BIN line: 2 for Best tagSNP, and 1 for tagSNP, and 0 for other SNP. LD_BIN_BOUNDARIES line: always "." strand always "+" frame always "." attributes This column contains the following items - ld_bin: LD bin name - RSID: RefSNP ID (rs number) - tagging: flag that indicates tagSNP - besttag: flag that indicates Best tagSNP - SNPID: unique ID given by Affymetrix (e.g. ld_bin 3R80M5Z_10_2 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)

prositeLisAC PROSITE DO PROSITE Info Link to PROSITE Information from prositeLisAC (simple search only) prositeLisFamilySize Number of ACs for this PROSITE DO prositeLisDE Description of this PROSITE DO prositeLisPatternSize Number of "Pattern" ACs for this PROSITE DO prositeLisRuleSize Number of "Rule" ACs for this PROSITE DO prositeLisRuleWithPASize Number of "Pattern" and "Rule" ACs for this PROSITE DO prositeLisRuleWithMASize Number of "Matrix" and "Rule" ACs for this PROSITE DO prositeLisMatrixSize Number of "Matrix" ACs for this PROSITE DO prosite3dLisIdSize Number of PDB entries for this PROSITE DO (in PROSITE) prosite3dSeqIdLisSize Number of PDB entries whose SEQRES matches this PROSITE DO prosite3dSeqChainLisSize Number of PDB chains whose SEQRES matches this PROSITE DO prosite3dAtomIdLisSize Number of PDB entries whose ATOM matches this PROSITE DO prosite3dAtomChainLisSize Number of PDB chains whose ATOM matches this PROSITE DO

prositeAC PROSITE Accession PDB SEQRES Link to PROSITE - PDB SEQRES matching from prositeAC (simple search only) prositeID PROSITE ID prositeIDType Accession type prositeDE Description of this entry prositeDO PROSITE DO of this entry prosite3dSize Number of PDB entries for this entry (in PROSITE) prosite3dSeqIdSize Number of PDB entries whose SEQRES matches this entry prosite3dSeqChainSize Number of PDB chains whose SEQRES matches this entry prosite3dAtomIdSize Number of PDB entries whose ATOM matches this entry prosite3dAtomChainSize Number of PDB chains whose ATOM matches this entry

prositeAC PROSITE Accession pdbID PDB ID pdbChain PDB chain pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this PROSITE entry

blocksFamilyAC BLOCKS Family Accession BLOCKS Info Link to BLOCKS Information from blocksFamilyAC (simple search only) blocksType Origing of this entry (PRINTS or PROTMAT) blocksFamilySize Number of ACs for this family accession blocksPrints PRINTS Accession (only from PRINTS) blocksName Description of this entry blocks3dIdFamilySize Number of PDB entries annotated with this entry by MAST blocks3dChainFamilySize Number of PDB chains annotated with this entry by MAST blocks3dSeqIdFamilySize Number of PDB entries whose SEQRES matches this entry blocks3dSeqChainFamilySize Number of PDB chains whose SEQRES matches this entry blocks3dAtomIdFamilySize Number of PDB entries whose ATOM matches this entry blocks3dAtomChainFamilySize Number of PDB chains whose ATOM matches this entry

blocksAC BLOCKS Accession PDB SEQRES Link to BLOCKS - PDB SEQRES matching from BLOCKS AC (simple search only) PDB ATOM Link to BLOCKS - PDB ATOM matching from BLOCKS AC (simple search only) blocksACFamily BLOCKS Family Accession Family VS PDB Link to BLOCKS - matching from BLOCKS AC Family (simple search only) blocksID BLOCKS ID blocksDE Description of this entry blocks3dIdSize Number of PDB entries annotated with this entry by MAST blocks3dChainSize Number of PDB chains annotated with this entry by MAST blocks3dSeqIdSize Number of PDB entries whose SEQRES matches this entry blocks3dSeqChainSize Number of PDB chains whose SEQRES matches this entry blocks3dAtomIdSize Number of PDB entries whose ATOM matches this entry blocks3dAtomChainSize Number of PDB chains whose ATOM matches this entry

blocksFamilyAC BLOCKS Family Accession pdbID PDB ID pdbChain PDB Chain

blocksFamilyAC BLOCKS Accession pdbID PDB ID pdbChain PDB Chain pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this BLOCKS entry

blocksFamilyAC BLOCKS Accession pdbID PDB ID pdbChain PDB Chain pdbIndex ATOM Start position pdbMatchLine Sequence numbers of PDB entries/chains whose SEQRES matches this BLOCKS entry

dbQSNP_id dbQSNP ID. strand Orientation of the STS compared with contig sequence of GenBank (NT sequence, NCBI Build 36) . Note that SNPs are always described as sequences in forward strand of the STS. contig_id ID of genomic contigs that showed highest homology to the STS (NT sequence, NCBI Build 36) rs# dbSNP accession for the refSNP (dbSNP Build 128) allele_1 sequence of allele 1 allele_2 sequence of allele 2 AF_allele_1 allele frequency of allele 1 AF_allele_2 allele frequency of allele 2 pool_id ID of pooled DNA (see below, DNA samples were extracted from peripheral blood lymphocytes) "CAU200", prepared from Caucasian Panel of 200, obtained from CORIELL (HD200, https://www.coriell.org) was used as the Caucasian pool in a large part of this study. "CP" (combined CEPH parents, prepared by us from 45 CEPH core family collection) and "COP" (HD100 from CORIELL) were also used. "JSA426", prepared from DNA derived from apparently healthy individuals enrolled at Kyushu area was used as the Japanese pool in a large part of study. Other pools derived from healthy individuals enrolled at various area of Japan were also used. Those were; JPK, JPK2, JPK3, JCM253, NCEP, NCL_P, NCP269, NCE_SP and JNCL_SP. The allele frequency data of pools derived from breast cancer patients (BREP, BRLP, JBRE_SP, JBRL_SP) and pools derived from systemic lupus erythematosus patients (SLEP264, SLEP183), obtained in association studies of each diseases, are also included #individual The number of individuals in the pool

dbQSNP_id dbQSNP ID. allele_Pos Variation allele position (1st base of variation) on the fasta sequence. It is always the 5' length plus 1. total_Len Total number of bases of the fasta sequence, a sum of length of 5', 3' and variation (A length of variation can be more than 1 in the case of ins/del polymorphisms). Internal_STS_ID Internal STS ID alleles Lists alleles of the SNP separated by '/'. sequence Sequence

ID experiment ID Post-genomic approache experimental method Stress experimental condition Data file (GEO) Registered ID in GEO Data file (CSV) Name of data file in CSV format Data file (Excel) Name of data file in Excel format Simple search Table in the simple search site Reference (PubMed) PubMed ID of reference

ORF Systematic Name in SGD（Saccharomyces Genome Database；http://www.yeastgenome.org/) GENE Standard Gene Name in SGD Growth rate YM/YW Rate of growth in YPD medium (Mutant/Wild-type） Growth rate SM/SW Rate of growth in YPD medium containing 30% sucrose (Mutant/Wild-type） DESCRIPTION (MIPS) Description in MIPS（Munich Information Center for Protein Sequences）

ORF Systematic Name in SGD（Saccharomyces Genome Database；http://www.yeastgenome.org/） GENE Standard Gene Name in SGD Growth rate BM/BW Rate of growth in non-strees condition （Mutant/Wild-type） Growth rate (AM/AW)/(BM/BW) AM/AW represents rate of growth after exposure to freeze-thaw strees (Mutant/Wild-type), (AM/AW)/(BM/BW) represents rate of AM/AW to BM/BW DESCRIPTION (MIPS) Description in MIPS（Munich Information Center for Protein Sequences）

ORF Systematic Name in SGD (Saccharomyces Genome Database；http://www.yeastgenome.org/) GENE Standard Gene Name in SGD Growth rate BM/BW Rate of growth in non-stress condition (Mutant/Wild-type) Growth rate (DM/DW)/(BM/BW) DM/DW represents rate of growth after exposure to air-drying stress (Mutant/Wild-type). (DM/DW)/(BM/BW) represents rate of DM/DW to BM/BW. DESCRIPTION (MIPS) Description in MIPS（Munich Information Center for Protein Sequences)

IDs and Links Library 14 different sequenced cDNA libraries (AF, AH, CF, CH, FC, FC-IC, FCL, SF, SH, SL, SS, VF, VH and VS) derived from five developmental stages. Clone ID ID of cDNA clone Atlas ID ID of Atlas database (http://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html) and link to Atlas database NBRP ID ID of cDNA clone covering full-length ORF provided by the National BioResource Project (http://www.nbrp.jp/). The link to the "National BioResource Project (NBRP) Dictyostelium discoideum" gene database (http://nenkin.lab.nig.ac.jp/genes?locale=en) is provided in the TogoDB edition. dictyBase ID ID of Protein Coding Gene in dictyBase (http://dictybase.org/). The link to dictyBase is provided in the TogoDB edition. Link to Contig Link to contig containing EST (TogoDB edition only) Representative Seq. and Annotation Representative seq. ID ID of DNA sequence used in homology search. Among these sequences, one sequence is selected as the representative DNA sequence by prioritizing 1) full-length cDNA sequence, 2) 5' EST-3'EST-ligated sequence, 3) 5' EST sequence and 4) 3' EST sequence in this order. Representative DNA sequence Representative DNA sequence sequence update Last update of representative DNA sequence Translated Amino Acid sequence Amino acid sequence translated from representative DNA sequence Translated Amino Acid sequence (All Frames) Amino acid sequences resulting from translation in all six reading frames of DNA sequence Homology vs CSM-cDNA List of top 10 hits in blastn search against the clone sequence in dicty_cDB own update Last update of homology search against CSM (a set of clone sequences) Homology vs DNA List of top 10 hits in blastn search against DNA sequences in public database dna update Last update of homology search against DNA sequences in public database Homology vs Protein List of top 10 hits in blastx search against protein sequences in public database protein update Last update of homology search against protein sequences in public database PSORT The results of PSORT (http://psort.ims.u-tokyo.ac.jp/), which is a program to predict the subcellular localization of proteins. Seqeunces 5' end seq. ID ID of 5' EST sequence. "F" is added to the end of ID. 5' end seq. 5' EST sequence. FASTA format. Length of 5' end seq. Length of 5' EST sequence. 3' end seq. ID ID of 3' EST sequence. "Z" is added to the end of ID. 3' end seq. 3' EST sequence. FASTA format. Length of 3' end seq. Length of 3' EST sequence. Connected seq. ID ID of 5' EST-3' EST-ligated sequence. "P" is added to the end of ID. Connected seq. Sequence of 5' EST ligated to 3' EST by 10 gaps (-). Length of connected seq. ID of 5' EST-3' EST-ligated sequence. (Gap (-) are not counted.) Full length Seq ID ID of full-length cDNA. "E" is added to the end of ID. Full length Seq. Full-length cDNA sequence. FASTA format. Length of full length seq. Length of full-length cDNA.

Contig information Contig ID ID of contig sequence Contig update Last update of sequence Contig sequence Contig sequence Gap Presence of gap (-) in contig. -If gap is included: gap included. -If gap is not included: no gap. Contig length Length of contig Chromosome number (1..6, M) Chromosome number of the chromosome to which the contig is mapped. If mapped, numbers 1 to 6 or M (mitochondria) will be used. Chromosome length Length of the chromosome to which the contig is mapped. Start point Start position of the contig mapped to the genome. End point End position of the contig mapped to the genome. Strand (PLUS/MINUS) Direction of the contig mapped to the genome (PLUS/MINUS) Number of clones Number of clones constituting the contig Number of EST Number of ESTs constituting the contig Link to clone list Link of all clones constituting contig to TogoDB edition. Link to the clone list is provided in the TogoDB edition only. List of clone(s) List of clones constituting contig. Link to each clone is provided in the TogoDB edition only. Annotation Translated Amino Acid sequence Representative amino acid sequence translated from DNA sequence. Translated Amino Acid sequence (All Frames) Amino acid sequences resulting from translation in all six reading frames of DNA sequence. own update Last update of blastn search against contig sequences in dicty_cDB. Homology vs CSM-cDNA List of top 10 hits in blastn search against contig sequences in dicty_cDB. dna update Last update of blastn search against DNA sequences in public database. Homology vs DNA List of top 10 hits in the results of blastn search against DNA sequences in public database. protein update Last update of blastx search against protein sequences in public database. Homology vs Protein List of top 10 hits in the results of blastx search against protein sequences in public database. PSORT The results of running PSORT(http://psort.ims.u-tokyo.ac.jp/), which is the program to predict the localization of proteins in the cell. Expression profile VS (DIR, S) Number of VS-derived clones constituting the contig VH (FL, L) Number of VH-derived clones constituting the contig VF (FL, S) Number of VF-derived clones constituting the contig AH (FL, L) Number of AH-derived clones constituting the contig AF (FL, S) Number of AF-derived clones constituting the contig SL (DIR, L) Number of SL-derived clones constituting the contig SS (DIR, S) Number of SS-derived clones constituting the contig SH (FL, L) Number of SH-derived clones constituting the contig SF (FL, S) Number of SF-derived clones constituting the contig CH (FL, L) Number of CH-derived clones constituting the contig CF (FL, S) Number of CF-derived clones constituting the contig FCL (DIR, L) Number of FCL-derived clones constituting the contig FC (DIR, S) Number of FC-derived clones constituting the contig FC-IC (SUB) Number of FC-IC-derived clones constituting the contig

cDNA library name Names of cDNA libraries (AF, AH, CF, CH, FC, FC-IC, FCL, SF, SH, SL, SS, VF, VH and VS) stages of the life cycle Stages in the life cycle of Dictyostelium discoideum 1) vegetatively growing cells (Vegetative phase)(V) 2) asexually developing cells at the aggregating (Aggregation phase)(A) 3) slug cells (Slug phase)(S) 4) culminating stages (Morphogenetic phase)(C) 5) sexually fusion-competent KAX3 cells (Gamete phase) (F) cDNA library construction method How to construct cDNA library 1) Conventional oligo-d(T) primed, directional cDNA libraries (dir) 2) Full-length cDNA libraries (oligocapped method)(fl) 3) Gamete-specific subtraction library (sub) cDNA library construction protocol Link to the webpage describing the protocol for generating cDNA library Size fractionation Size fractionation of clone 1) Fractionation of long clone (long) 2) Fractionation of short clone (short) 3) No fractionation (no) clone size Clone size(kb)

PubmedID PubMed ID (PMID) of article Title Article title Authors Article author(s) Publication Journal published the article Pathway Diagram of the pathway (Blank in the downloaded data) PNG File Link to the pathway diagram (PNG file) (In the downloaded data, a flag indicating the existence of the diagram is shown.) SVG File Link to the pathway diagram (SVG file) (In the downloaded data, a flag indicating the existence of the diagram is shown.) HTML File Link to the pathway information (HTML file) (In the downloaded data, a flag indicating the existence of the information is shown.) CSML File Link to the pathway information (CSML file) (In the downloaded data, a flag indicating the existence of the information is shown.) Open .csml file with CIOPlayer Link to open a CSML file on Cell Illustrator Online Player (Blank in the downloaded data.) Open .csml file with CIO Link to open a CSML file at Cell Illustrator Online (Blank in the downloaded data.)

JW_ID Gene ID assigned by GenoBase to the E. coli strain K-12 substrain W3110. ECK number Accession number which can refer to genes in both substrains MG1655 and W3110 of the E. coli strain K-12. B number Gene accession number assigned by the Blattner laboratory to the E. coli strain K-12 substrain MG1655. Gene name K-12 Gene name of the E. coli strain K-12. Locus name K-12 Locus name of the E. coli strain K-12. Synonyms of locus names K-12 Synonyms of the locus name of the E. coli strain K-12. Solubility (%) Solubility determined in Niwa et. al., PNAS 2009. (unit: %) Yield (uM) Yield of the protein measured in Niwa et. al., PNAS 2009. (unit: μM) Yield (ug/ml) Yield of the protein measured in Niwa et. al., PNAS 2009. (unit: μg/ml) Minus Sol (%) Solubility in the absence of any chaperons. (unit: %) It is redetermined to evaluate chaperon effects. TF Sol (%) Solubility in the presence of Trigger Factor. (unit: %) GroE Sol (%) Solubility in the presence of GroEL/ES. (unit: %) KJE Sol (%) Solubility in the presence of DnaK/DnaJ/GrpE. (unit: %) Minus Yield (uM) Yield in the absence of any chaperons. (unit: μM) TF Yield (uM) Yield in the presence of Trigger Factor. (unit: μM) GroE Yield (uM) Yield in the presence of GroEL/ES. (unit: μM) KJE Yield (uM) Yield in the presence of DnaK/DnaJ/GrpE. (unit: μM) Minus Yield (ug/ml) Yield in the absence of any chaperons. (unit: μg/ml) TF Yield (ug/ml) Yield in the presence of Trigger Factor. (unit: μg/ml) GroE Yield (ug/ml) Yield in the presence of GroEL/ES. (unit: μg/ml) KJE Yield (ug/ml) Yield in the presence of DnaK/DnaJ/GrpE. (unit: μg/ml) Calculated MW (kDa) Molecular weight calculated from amino acid sequences. (unit: kDa) Calculated pI Isoelectric point calculated from amino acid sequences. Type of gene product Type of gene product obtained from Genobase. (About the description of "Type of gene product", see this page.) Gene product description Description obtained from Genobase. Cell location Localization in the cell. Structure (PDB) ID PDB ID obtained from Genobase. SCOP assignment SCOP assignment obtained from Genobase.

Extract name Internal ID FF ontology Ontology ID in FANTOM Description Description Catalog ID RNA catalog ID Category Category Species Species Sex Sex Age Age Developmental stage Developmental stage Tissue Tissue Cell lot Cell lot Cell type Cell type Catalogue ID Cell catalogue ID Collaboration Collaboration Provider Cell provider Extraction protocol RNA extraction protocol Material type RNA Material type RNA tube RNA tube ID (the same as Extact name) Sample name Sample name RNA extraction RNA extraction RNA ID Internal RNA ID Comment on RNA Comment on RNA ratio_260/230 Ratio (260nm/230nm) of the sample ratio_260/280 Ratio (260nm/280nm) of the sample Concentration RNA concentration RNA Integrity number RNA Integrity number lsid Sample group ID Library protocol Library protocol Library ID Library ID Sequence protocol Sequence protocol Machine name Machine name Run name Run name Flowcell channel Flowcell channel Alignment protocol Alignment protocol BAM file Read mapping results (BAM format) BAI file Index of BAM file CAGE TSS file TSS identified by CAGE analysis (BED format) Ribosomal DNA sequence file rDNA sequence file (FASTA format) Barcode Barcode sequence for RNA sample identification

Extract name Internal ID FF ontology Ontology ID in FANTOM Description Description Catalog ID RNA catalog ID Category Category Species Species Sex Sex Age Age Developmental stage Developmental stage Tissue Tissue Cell lot Cell lot Cell type Cell type Catalogue ID Cell catalogue ID Collaboration Collaboration Provider Cell provider Extraction protocol RNA extraction protocol Material type RNA Material type RNA tube RNA tube ID (the same as Extact name) Sample name Sample name RNA extraction RNA extraction RNA ID Internal RNA ID Comment on RNA Comment on RNA ratio_260/230 Ratio (260nm/230nm) of the sample ratio_260/280 Ratio (260nm/280nm) of the sample Concentration RNA concentration lsid RNA Integrity number Library protocol Library protocol Library ID Library ID Sequence protocol Sequence protocol Machine name Machine name Run name Run name Flowcell channel Flowcell channel Alignment protocol Alignment protocol BAM file Read mapping results (BAM format) BAI file Index of BAM file CAGE TSS file TSS identified by CAGE analysis (BED format) Ribosomal DNA sequence file rDNA sequence file (FASTA format)

Library ID DNA sequence library ID FF ontology Ontology ID defined in FANTOM DRA sample accession number DRA sample accession number DRA experiment accession number DRA experiment accession number DRA run accession number DRA run accession number DRA analysis accession number (BAM) DRA analysis accession number (BAM) DRA analysis accession number (BED) DRA analysis accession number (BED) Experiment method Experiment method

Library ID DNA sequence library ID Raw Measured reads Removed by extraction Removed reads by extraction Extracted Extracted reads by analysis Removed by artifacts Removed artifatcts Filtered for artifact Reads filterd for artifacts Removed by rRNA Removed reads as rRNA Filtered for rRNA Reads filterd for rRNAs Non alignment Reads not mapped on genome Genome mapped Reads mapped on genome Duplicated Duplicated reads Uniquely mapped Unique reads Inproperly mapped pairs Read pairs inproperly mapped on genome Properly mapped pairs Read pairs properly mapped on genome Total pairs Total pairs Exon Pairs on exon Intergenic Pairs on intergenic Promoter Pairs on promoter

FA ID Review ID URL Review URL Title Review Title Date Publication date Author(s) Review author(s) DOI Review DOI Original article title Original article title Original article author(s) Original article author(s) Original journal Original journal Original article number Original article number Content Review content (HTML) Tags Tags to the review Fig1 Fig1 caption (Link to the Fig1 file in simple search) Fig2 Fig2 caption (Link to the Fig2 file in simple search) Fig3 Fig3 caption (Link to the Fig3 file in simple search) Fig4 Fig4 caption (Link to the Fig4 file in simple search) doc file doc file name (Link to the file in simple search) txt file txt file name (Link to the file in simple search)

ID Entry ID Accession Accession Description Description SO name Sequence Ontology Organism Organism Xref Cross Reference Length Sequence Length Sequence Sequence Second Structure Thumbnail Thumbnail of RNA secondary structure image Second Structure (PNG) RNA secondary structure image (PNG) Second Structure (PDF) RNA secondary structure image (PDF)

Sequence ID ID of a sequence Cluster ID ID of cluster. gclust_cluster is referenced. Annotation in original database Annotation at the original website Species Species name Length Amino acid sequence length Sequence Amino acid sequence

Cluster ID ID of cluster Representative sequence ID ID of a sequence that represents the cluster. gclust_seq is referenced. Link to cluster sequences Link to the list of sequences belonging to the cluster (empty space) Link to related sequences Link to the list of sequences that are similar to the cluster, but not clustered Sequence length Amino acid sequence length Representative annotation Representative annotation of the cluster Number of Sequences Number of sequences contained in the cluster Homologs Number of sequences contained in the cluster Clustering threshold The threshold of E-value used for clustering Plants (7species) (%) The appearance rate of this cluster in the plant and algal group (including 7 species) Other bikonts (9 species) (%) The appearance rate of this cluster in other Bikonta (Chromalveolata, Excavata) group (including 9 species) Cyano (25species) (%) The appearance rate of this cluster in the cyanobacteria group (including 25 species) Photo Bact (15species) (%) The appearance rate of this cluster in the photosynthetic bacteria group (including 15 species) Other Bact (31 species) (%) The appearance rate of this cluster in the non-photosynthetic bacteria group (including 31 species) Opisthokonts (8species) (%) The appearance rate of this cluster in the opisthokont group (including 8 species) Number of Sequences for each species The number of sequences by organism species contained in the cluster Species not appearing in this cluster Organism species not contained in the cluster

Cluster ID ID of cluster Sequence ID ID of a sequence

Field 1 ID of amino acid sequence (Sequence ID) Field 2 Length of amino acid sequence Field 3 Annotation of amino acid sequence

ATH Arabidopsis thaliana CME Cyanidioschyzon merolae CRE Chlamydomonas reinhardtii OSA Oryza sativa OTAU Ostreococcus tauri PPT Physcomitrella patens PoTR Populus tricocarpa DPTM Paramecium tetraurelia GTH Guillardia theta NGR Naegleria gruberi PFA Plasmodium falciparum PHRA Phytophthora ramorum PHSO Phytophthora sojae PTR Phaeodactylum tricornutum TET Tetrahymena thermophila SB210 TPS Thalassiosira pseudonana Ana Anabaena sp. PCC 7120 Ava Anabaena variabilis ATCC 29413 Glv Gloeobacter violaceus Npun Nostoc punctiforme sp. PCC73102 Pm1 Prochlorococcus marinus MED4 Pm2 Prochlorococcus marinus MIT9313 Pm3 Prochlorococcus marinus SS120 Pm4 Prochlorococcus marinus MIT9312 Pm5 Prochlorococcus marinus NATL2A Pm6 Prochlorococcus marinus MIT9301 Pm7 Prochlorococcus marinus MIT9303 Pm8 Prochlorococcus marinus MIT9315 Pm9 Prochlorococcus marinus NATL1A PmA Prochlorococcus marinus AS9601 S63 Synechococcus sp. PCC 6301 S79 Synechococcus sp. PCC 7942 S81 Synechococcus sp. WH8102 S93 Synechococcus sp. CC9311 S96 Synechococcus sp. CC9605 Syn Synechocystis sp. PCC 6803 Tel Thermosynechococcus elongatus Ter Trichodesmium erythraeum 405 1 YelA Cyanobacterium Yellowstone A-prime YelB Cyanobacterium Yellowstone B-prime Caur Chloroflexus aurantiacus Cch Chlorobium chlorochromatii CaD3 Clim Chlorobium limicola DSM 245 Cph Chlorobium phaeobacteroides DSM 266 Ctep Clorobium tepidum Pvi Prostheocochloris vibrioformis DSM 265 Rde Roseobacter denitrificans Och 114 Rpa1 Rhodopseudomonas plustris BisA53 Rpa2 Rhodopseudomonas plustris BisB4 Rpa3 Rhodopseudomonas plustris BisB18 Rpa4 Rhodopseudomonas plustris HaA2 Rpal Rhodopseudomonas plustris Rrub Rhodospirillum rubrum ATCC 11170 Rsh Rhodobacter sphaeroides ATCC 17029 Rsp Rhodobacter sphaeroides 2.4.1 Afu Archaeoglobus fulgidus DSM 4304 Ape Aeropyrum pernix K1 Atu Agrobacterium tumefaciens str. C58 Bja Bradyrhizobium japonicum USDA 110 Bma Burkholderia mallei ATCC 23344 Bms Brucella suis 1330 Bpe Bordetella pertussis Tohama I Bsu Bacillus subtilis Marburg 168 Ccr Caulobacter crescentus CB15 Cvi Chromobacterium violaceum ATCC 12472 Eba Azoarcus sp EbN1 Eco Escherichia coli K-12 Fal Frankia alni ACN14a Fra Frankia sp. CcI3 Gox Gluconobacter_oxydans_621H Hal Halobacterium sp. NRC-1 Mac Methanosarcina acetivorans str. C2A Mes Mesorhizobium sp. BNC1 Mlo Mesorhizobium loti MAFF303099 Mtu Mycobacterium tuberculosis H37Rv Neq Nanoarchaeum equitans Kin4-M Pho Pyrococcus horikoshii OT3 Pst Pseudomonas syringae pv. tomato str. DC3000 Rhe Rhizobium_etli_CFN_42 Rle Rhizobium leguminosarum Rso Ralstonia solanacearum GMI1000 Sco Streptomyces coelicolor A3(2) Sep Staphylococcus epidermidis ATCC 12228 Sme Sinorhizobium meliloti 1021 Sto Sulfolobus tokodaii str. 7 Vvy Vibrio vulnificus YJ016 CEL Caenorhabditis elegans DCGR Candida glabrata CBS138 DKLA Kluyveromyces lactis NRRL Y-1140 DME Drosophila melanogaster HSA Homo sapiens SPO Schyzosaccharomyces pombe S99 Synechococcus sp. CC9902 NCR Neurospora crassa 74-OR23-1A SCE Saccharomyces cerevisiae

Field 1 Prefix of the sequence ID of organism Field 2 Group (Numbers from 1 to 6)

Field 1 Group number Field 2 Designated value for allocation to organism group Field 3 Group name

Number Cluster ID ID Sequence ID Length Sequence length seqs Number of sequences belonging to cluster homologs Number of sequences belonging to cluster ATH Number of sequences belonging to cluster in the Arabidopsis thaliana sequence OSA Number of sequences belonging to cluster in the Oryza sativa sequence PoTR Number of sequences belonging to cluster in the Populus tricocarpa sequence PPT Number of sequences belonging to cluster in the Physcomitrella patens sequence CRE Number of sequences belonging to cluster in the Chlamydomonas reinhardtii sequence OTAU Number of sequences belonging to cluster in the Ostreococcus tauri sequence CME Number of sequences belonging to cluster in the Cyanidioschyzon merolae sequence GTH Number of sequences belonging to cluster in the Guillardia theta sequence PFA Number of sequences belonging to cluster in the Plasmodium falciparum sequence PTR Number of sequences belonging to cluster in the Phaeodactylum tricornutum sequence TPS Number of sequences belonging to cluster in the Thalassiosira pseudonana sequence Ter Number of sequences belonging to cluster in the Trichodesmium erythraeum 405 1 sequence Ana Number of sequences belonging to cluster in the Anabaena sp. PCC 7120 sequence Ava Number of sequences belonging to cluster in the Anabaena variabilis ATCC 29413 sequence Npun Number of sequences belonging to cluster in the Nostoc punctiforme sp. PCC73102 sequence Syn Number of sequences belonging to cluster in the Synechocystis sp. PCC 6803 sequence Glv Number of sequences belonging to cluster in the Gloeobacter violaceus sequence Tel Number of sequences belonging to cluster in the Thermosynechococcus elongatus sequence YelA Number of sequences belonging to cluster in the Cyanobacterium Yellowstone A-prime sequence YelB Number of sequences belonging to cluster in the Cyanobacterium Yellowstone B-prime sequence S63 Number of sequences belonging to cluster in the Synechococcus sp. PCC 6301 sequence S79 Number of sequences belonging to cluster in the Synechococcus sp. PCC 7942 sequence S81 Number of sequences belonging to cluster in the Synechococcus sp. WH8102 sequence S93 Number of sequences belonging to cluster in the Synechococcus sp. CC9311 sequence S96 Number of sequences belonging to cluster in the Synechococcus sp. CC9605 sequence S99 Number of sequences belonging to cluster in the Synechococcus sp. CC9902 sequence Pm1 Number of sequences belonging to cluster in the Prochlorococcus marinus MED4 sequence Pm2 Number of sequences belonging to cluster in the Prochlorococcus marinus MIT9313 sequence Pm3 Number of sequences belonging to cluster in the Prochlorococcus marinus SS120 sequence Pm4 Number of sequences belonging to cluster in the Prochlorococcus marinus MIT9312 sequence Pm5 Number of sequences belonging to cluster in the Prochlorococcus marinus NATL2A sequence Pm6 Number of sequences belonging to cluster in the Prochlorococcus marinus MIT9301 sequence Pm7 Number of sequences belonging to cluster in the Prochlorococcus marinus MIT9303 sequence Pm8 Number of sequences belonging to cluster in the Prochlorococcus marinus MIT9315 sequence Pm9 Number of sequences belonging to cluster in the Prochlorococcus marinus NATL1A sequence PmA Number of sequences belonging to cluster in the Prochlorococcus marinus AS9601 sequence Atu Number of sequences belonging to cluster in the Agrobacterium tumefaciens str. C58 sequence Bja Number of sequences belonging to cluster in the Bradyrhizobium japonicum USDA 110 sequence Bms Number of sequences belonging to cluster in the Brucella suis 1330 sequence Ccr Number of sequences belonging to cluster in the Caulobacter crescentus CB15 sequence Gox Number of sequences belonging to cluster in the Gluconobacter_oxydans_621H sequence Mes Number of sequences belonging to cluster in the Mesorhizobium sp. BNC1 sequence Mlo Number of sequences belonging to cluster in the Mesorhizobium loti MAFF303099 sequence Rhe Number of sequences belonging to cluster in the Rhizobium_etli_CFN_42 sequence Rle Number of sequences belonging to cluster in the Rhizobium leguminosarum sequence Sme Number of sequences belonging to cluster in the Sinorhizobium meliloti 1021 sequence Rpa1 Number of sequences belonging to cluster in the Rhodopseudomonas plustris BisA53 sequence Rpa2 Number of sequences belonging to cluster in the Rhodopseudomonas plustris BisB4 sequence Rpa3 Number of sequences belonging to cluster in the Rhodopseudomonas plustris BisB18 sequence Rpa4 Number of sequences belonging to cluster in the Rhodopseudomonas plustris HaA2 sequence Rpal Number of sequences belonging to cluster in the Rhodopseudomonas plustris sequence Rrub Number of sequences belonging to cluster in the Rhodospirillum rubrum ATCC 11170 sequence Rde Number of sequences belonging to cluster in the Roseobacter denitrificans Och 114 sequence Rsh Number of sequences belonging to cluster in the Rhodobacter sphaeroides ATCC 17029 sequence Rsp Number of sequences belonging to cluster in the Rhodobacter sphaeroides 2.4.1 sequence Eco Number of sequences belonging to cluster in the Escherichia coli K-12 sequence Pst Number of sequences belonging to cluster in the Pseudomonas syringae pv. tomato str. DC3000 sequence Vvy Number of sequences belonging to cluster in the Vibrio vulnificus YJ016 sequence Bsu Number of sequences belonging to cluster in the Bacillus subtilis Marburg 168 sequence Sep Number of sequences belonging to cluster in the Staphylococcus epidermidis ATCC 12228 sequence Fal Number of sequences belonging to cluster in the Frankia alni ACN14a sequence Fra Number of sequences belonging to cluster in the Frankia sp. CcI3 sequence Mtu Number of sequences belonging to cluster in the Mycobacterium tuberculosis H37Rv sequence Sco Number of sequences belonging to cluster in the Streptomyces coelicolor A3(2) sequence Rso Number of sequences belonging to cluster in the Ralstonia solanacearum GMI1000 sequence Cvi Number of sequences belonging to cluster in the Chromobacterium violaceum ATCC 12472 sequence Bma Number of sequences belonging to cluster in the Burkholderia mallei ATCC 23344 sequence Bpe Number of sequences belonging to cluster in the Bordetella pertussis Tohama I sequence Eba Number of sequences belonging to cluster in the Azoarcus sp EbN1 sequence Caur Number of sequences belonging to cluster in the Chloroflexus aurantiacus sequence Cch Number of sequences belonging to cluster in the Chlorobium chlorochromatii CaD3 sequence Clim Number of sequences belonging to cluster in the Chlorobium limicola DSM 245 sequence Cph Number of sequences belonging to cluster in the Chlorobium phaeobacteroides DSM 266 sequence Ctep Number of sequences belonging to cluster in the Clorobium tepidum sequence Pvi Number of sequences belonging to cluster in the Prostheocochloris vibrioformis DSM 265 sequence Afu Number of sequences belonging to cluster in the Archaeoglobus fulgidus DSM 4304 sequence Hal Number of sequences belonging to cluster in the Halobacterium sp. NRC-1 sequence Mac Number of sequences belonging to cluster in the Methanosarcina acetivorans str. C2A sequence Pho Number of sequences belonging to cluster in the Pyrococcus horikoshii OT3 sequence Ape Number of sequences belonging to cluster in the Aeropyrum pernix K1 sequence Sto Number of sequences belonging to cluster in the Sulfolobus tokodaii str. 7 sequence Neq Number of sequences belonging to cluster in the Nanoarchaeum equitans Kin4-M sequence SCE Number of sequences belonging to cluster in the Saccharomyces cerevisiae sequence SPO Number of sequences belonging to cluster in the Schyzosaccharomyces pombe sequence PHRA Number of sequences belonging to cluster in the Phytophthora ramorum sequence PHSO Number of sequences belonging to cluster in the Phytophthora sojae sequence DCGR Number of sequences belonging to cluster in the Candida glabrata CBS138 sequenc DKLA Number of sequences belonging to cluster in the Kluyveromyces lactis NRRL Y-1140 sequence NCR Number of sequences belonging to cluster in the Neurospora crassa 74-OR23-1A sequence DPTM Number of sequences belonging to cluster in the Paramecium tetraurelia sequence TET Number of sequences belonging to cluster in the Tetrahymena thermophila SB210 sequence NGR Number of sequences belonging to cluster in the Naegleria gruberi sequence HSA Number of sequences belonging to cluster in the Homo sapiens sequence DME Number of sequences belonging to cluster in the Drosophila melanogaster sequence CEL Number of sequences belonging to cluster in the Caenorhabditis elegans sequence Annotations Annotation

SWISS-PROT_ID ID of SWISS-PROT EntrezGene_ID ID of EntrezGene Other_ID ID of databases other than above Gene_Name Gene name

ORF Name ORF Name ORF ID ORF ID Superkingdom Superkingdom of the species which contains this ORF Species The species which contains this ORF Chromosome The chromosome (Refseq ID) which contains this ORF Alignment (PDB & Intermediate Sequence) PDB ID and its corresponding intermediate sequence ID It links to the alignment information. Alignment (ORF & Intermediate Sequence) ORF Name and its corresponding intermediate sequence ID It links to the alignment information. Region in PDB (3D) The position of PDB 3D structure corresponding this ORF Prosite Motifs (in ORF)(in PDB) The PROSITE motif corresponding this ORF

Chromosome The chromosome (Refseq ID) which contains this ORF ORF ID ORF ID Header FASTA header of this sequence Sequence Sequence

Query PSI-BLAST search query (PDB ID) Alignment It links to the alignment result file.

Chromosome The chromosome (RefSeq ID) which contains this ORF Query BLAST search query (ORF ID) Alignment Alignment result

Gene ID ID of the gene Gene Symbol Symbol of the gene Gene Name Name of the gene Organism Organism of the gene Phenotype from JST bibliography Names of the diseases or the phenotypes that were extracted from the articles related to the gene MeSH Tree MeSH trees of the MeSH terms that are corresponding to the diseases or the phenotypes JST bibliography database IDs of the articles provided from the JST bibliographic information system (JDream II)

Line information DGRC Number Line number of DGRC (Drosophila Genetic Resource Center) (Link to DGRC in TogoDB) Genotype Genotype Insertion Site Insert site(s) on the physical map. For two or more insert sites, use semicolon to delimit each site (see http://www.dgrc.kit.jp/~jdd/chromosome/index.html). (Link to the DGRC genome viewer is created, and the download file has link tag.) Map Viewer DGRC Number (TogoDB has link to the DGRC genome viewer.) Related Genes Name of related gene Original Number Line number in GETDB Chr. Chromosome number Comments Comment Balancer Name of balancer chromosome Link to Clone Table Link to clone list (Empty column in downloaded file) Num of clones Number of clones Cluster id Cluster ID (two or more) Link to Cluster Table Cluster ID. Two or more IDs will be delimited by %7C ("|" decoded by UTF8). (Link to cluster table is available in TogoDB.) Num of clusters Number of clusters Stock Request Link to placing an order for the stock (Empty column in the downloaded file.) Expression information Embryonic Expression Information on expression in embryo Larval GFP Information on expression of GFP in larva Larval X-gal Information on expression of X-gal in larva Adult GFP Information on expression of GFP in adult Lethality Lethality Also known as Genotype alias Original Comments Original Comment (Comment by GETDB) Fluorescence expression image Disc(Image) Expression image in imaginal disc Disc (Number) Number of expression images in imaginal disc Embryo(Image) Expression image in embryo Embryo (Number) Number of expression images in embryo Larval GFP(Image) Fluorescence expression image in GFP-dyed larva Larval GFP (Number) Number of fluorescence expression images in GFP-dyed larva Adult(Image) Expression image in adult Adult (Number) Number of expression images in adult

Clone Name Name of the clone of the genome sequence adjacent to the 5'-end of the Drosophila GAL4 enhancer trap element DGRC Number Line number (Link to Strain Table in TogoDB) Cluster Id Cluster ID of genome insert coordinate (Link to Cluster Table in TogoDB) Strand Insert direction to genome sequence (*) Insertion Point Insert position on genome sequence (*) Chr. Band Chromosome band Flanking Sequence Adjacent sequence downstream of the insert point.

ClusterId Cluster ID of genome insert coordinate Cluster Member(Clone Name : Cluster Id) Clone name corresponding to each of the insert point sequences belonging to the cluster Cluster Size Number of insert coordinates belonging to the cluster. Link to Clone Table Cluster ID. (Link to CloneTable in TogoDB.) Link to Strain Table Cluster ID. (Link to Strain Table in TogoDB) Chr. Band Chromosome band Insertion Point (Min) Minimum value in the cluster of insert positions on genome sequence Insertion Point (Max) Maximum value in the cluster of insert positions on genome sequence Max-Min Maximum value minus minimum value of insert positions on genome sequence

No. Number, it will be changed in each update Family / Subfamily Family / Subfamily Tribe / Subtribe Tribe / Subtribe Genus Genus Species / Subspecies Species / Subspecies Variety Variety chromosome number n chromosome number n=（No. of plants examined) chromosome number 2n chromosome number 2n=(total karyotypic length)（No. of plants examined) Life form Life form Breeding system Breeding system Collected Locality Collected Locality Author name ＆ Published year Author name ＆ Published year Author Author Year Year Title Title Journal Journal Vol.(Number) Vol.(Number) Page Page

Pathway Name Name of signal transduction pathway INOH format Link to INOH format file BioPAX level2 format Link to BioPAX level2 format file BioPAX level3 format Link to BioPAX level3 format file PubMed ID Link to PubMed

Pathway Name Name of metabolic pathway INOH format Link to INOH format file BioPAX level2 format Link to BioPAX level2 format file BioPAX level3 format Link to BioPAX level3 format file

inoh_id ID of the term alt_id Altanative ID of the term name Name of the term synonym Synonym of the term def Definition of the term xref_analog Cross-reference to other ontology term comment Comment of the term linkage Image file that represents "is_a" and "part_of" relations between terms. inoh_client Link to start the INOH Client application. is_a Definition of "is_a" relation. relationship Definition of "part_of" relation. is_obsolete The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

inoh_id ID of the term alt_id Altanative ID of the term name Name of the term synonym Synonym of the term def Definition of the term xref_analog Cross-reference to other ontology term comment Comment of the term linkage Image file that represents "is_a" and "part_of" relations between terms. inoh_client Link to start the INOH Client application. is_a Definition of "is_a" relation. relationship Definition of "part_of" relation. is_obsolete The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

inoh_id ID of the term alt_id Altanative ID of the term name Name of the term synonym Synonym of the term def Definition of the term xref_analog Cross-reference to other ontology term comment Comment of the term linkage Image file that represents "is_a" and "part_of" relations between terms. inoh_client Link to start the INOH Client application. is_a Definition of "is_a" relation. relationship Definition of "part_of" relation. is_obsolete The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

AquaPro/RawBinary/*.prf AquaPro raw binary files AquaPro/ASCIIoutput/*.pra AquaPro ASCII output files pra file format Header line Month [1-12] Day [1-31] Year Hour [0-23] Minute [0-59] Second [0-59] Error code Status code Battrey voltage [V] Sound speed [m/s] Heading [degrees] Pitch [degrees] Roll [degrees] Pressure [dbar] Temperture [degrees C] Analog input 1 Analog input 2 Number of beams Number of cells Data lines (repeat below） Cell number Velocity (Beam 1) X|East [m/s] Velocity (Beam 2) Y|North [m/s] Velocity (Beam 3) Z|Up [m/s] Amplitude (Beam 1) [counts] Amplitude (Beam 2) [counts] Amplitude (Bean 3) [counts] AWAC/RawBinary/*.wpr AWAC raw binary files AWAC/ASCIIconvertedRAW/*.a[123] AWAC amplitude data (Beam 1, 2, 3) AWAC/ASCIIconvertedRAW/*.csv AWAC profile data (comma sepalated values format) AWAC/ASCIIconvertedRAW/*.dat AWAC velocity data AWAC/ASCIIconvertedRAW/*.hdr AWAC header file (each file format are described by ASCII) AWAC/ASCIIconvertedRAW/*.nmea AWAC raw data in NMEA format AWAC/ASCIIconvertedRAW/*.sen AWAC sensor data AWAC/ASCIIconvertedRAW/*.ssl AWAC system state file AWAC/ASCIIconvertedRAW/*.v[123] AWAC velocity data (Beam 1|X|East, Beam 2|Y|North, Beam 3|Z|Up) AWAC/ASCIIconvertedRAW/*.wad AWAC raw wave data AWAC/ASCIIconvertedRAW/*.whd AWAC wave header data

Raw/*.vec Raw data (binary) Raw/*.vea Raw data (ASCII) Processed/*.txt 1min. Processed data (ASCII) Format of txt file date Date (YYYY/MM/DD) time Time (hh:mm:ss) depth_m Depth [meter] press_dbar Pressure [dbar] temp_degC Temperature [degrees C] velE_m/s Velocity (East) [m/s] velN_m/s Velocity (North) [m/s] velU_m/s Velocity (Up) [m/s] corrE_% Correlation (East) [%] corrN_% Correlation (North) [%] corrU_% Correlation (Up) [%]

Date [YYYY/MM/DD] Time [hh:mm:ss.sss] pval Temperature [degrees C] Chlorophyll [ug/l] (microgram per litter) Turbidity [FTU] (Formazin Turbidity Unit) Power voltage [V]

Date [YYYY/MM/DD] Time [hh:mm:ss.sss] pval Conductivity [mS/cm] Temperature [degrees C] Salinity

Date [YYYY,MM,DD] Time [hh:mm:ss.sss] pval Temperature [degrees C] Dissolved Oxygen Concentration [%] Power voltage [V]

PNG Portable Network Graphics format WAV RIFF waveform Audio Format

Date [YYYY/MM/DD] Time [hh:mm:ss.sss] real N1 N2 N3 N4 N5 N6 p_label (pg) Photo Quantum [umol/m2/s] (micro-mol/m2/sec) v_label (v) Power voltage [V]

date Date [YYYY/MM/DD] time Time [hh:mm:ss.sss] id SATSLF0932 timefield YYYY+day of year (e.g., 2016332 = Nov.27, 2016) nitrate_um Nitrate [umol/L] (micro-mol per litter) nitrate_mg Nitrate [mg/L] (microgram per litter) Error t_lamp t_spec humidity Humidity volt_12 volt_reg volt_main spec_ave dark_ave ch1-226 chksum Checksum

date Date [YYYY/MM/DD] time Time [hh:mm:ss.sss] T01 Temperature at layer 1 T02 Temperature at layer 2 T03 Temperature at layer 3 T04 Temperature at layer 4 T05 Temperature at layer 5 T06 Temperature at layer 6 T07 Temperature at layer 7 T08 Temperature at layer 8 T09 Temperature at layer 9 T10 Temperature at layer 10 T11 Temperature at layer 11 T12 Temperature at layer 12 T13 Temperature at layer 13 T14 Temperature at layer 14 T15 Temperature at layer 15 T16 Temperature at layer 16 T17 Temperature at layer 17 T18 Temperature at layer 18 T19 Temperature at layer 19 T20 Temperature at layer 20 D01 unknown

Date [YYYY/MM/DD] Time [hh:mm:ss.sss] pval Depth [meter] Temperature [degrees C] Power voltage [V]

JPG image file（JPEG format）

institutionCode institution code collectionCode collection code catalogNumber number occurrenceID ID for a plankton image in the dataset occurrenceStatus biological occurrence status basisOfRecord basis of the record eventDate date time in ISO 8601 fomrmat [yyyy-mm-ddThh:mm:ss+|–hh:mm] decimalLatitude geographic latitude in decimal degrees decimalLongitude geographic longitude in decimal degrees minimumDepthInMeters the lesser depth of a range of depth below the sea surface maximumDepthInMeters the greater depth of a range of depth below the sea surface label biological name or object name associatedMedia file name of the image

protein_id jPOST internal protein ID accession UniProt ID symbol UniProt protein symbol name protein name protein_type protein type(Leading protein, Spectrum same-set protein Spectrum sub-set protein, Spectrum subsumable protein) pep_count identified peptide count psm_count peptide from psm(peptide specrum match) count uniq_pep_count unique peptide count

psm_id Internal PSM ID sequence peptide sequence accession UniProt ID exp_mz M/Z value(ratio between mass m and chage z) obtained by experiment calc_mz M/Z value(ratio between mass m and chage z) value obtained by calculation charge charge jpost_score jPOST score

psm_id Internal PSM ID modification modification type site modification site position position in peptide sequence

jPOST ID Project ID PXID ProtemoeXchange (PX) ID Project title Project title Keywords Keywords Description Description Mode Data analysis mode ("Complete" or "Partial") PubMed ID(s) PubMed ID(s) if articles are published PubMed Info References if articles are published Principal investigator Principal investigator Created date Data registration date Announcement date Data publication date Note Note Contact Contact Revision Revision Files Registered file list (Only simple search)

jPOST ID Project ID File ID File ID File Name File Name Download Download link (Only simple search) File size File size Profiles The list of profiles in this file (Only simple search)

jPOST ID Project ID File ID File ID Profile plex Profile name Sample - ID Sample ID Sample - Title Sample name Fractionation - ID Fractionation ID Fractionation - Title Fractionation name Enzyme/Mod. - ID Enzyme/Mod. reaction ID Enzyme/Mod. - Title Enzyme/Mod. reaction name MS mode - ID MS mode ID MS mode - Title MS mode name

ID Sample ID Title Sample name Species Species Tissue Tissue Cell type Cell type Disease Disease Note Note

ID Fractionation ID Title Fractionation name Subcellular Subcellular Protein Protein Peptide Peptide Note Note

ID Enzyme/Mod. reaction ID Title Enzyme/Mod. reaction name Enzyme Enzyme Fixed modification Modification prepared before the experiment Variable modification Other modifications Taxonomy Taxonomy Note Note

ID MS mode ID Title MS mode name Instrument Instrument Instrument mode Instrument mode Purpose Purpose Quantification platform Quantification platform Plex Plex Label Label Note Note

Database Name database name JSNP_SNP: single nucleotide polymorphism JSNP_InsDel_IND: insertion/deletion JSNP_InsDel_MIC: microsatelite JSNP ID JSNP ID ID starting with IMS-JST: from IMS and JST ID starting with ssj: from RIKEN SNP Research Center or from Tokyo Women's Medical University Allele Frequency (only in SimpleSearch pages) link to Allele Frequency of the same JSNP ID Screening Information (only in SimpleSearch pages) link to Screening Information of the same JSNP ID Mapping Information (only in SimpleSearch pages) link to Mapping Information of the same JSNP ID Integrated List (only in SimpleSearch pages) link to Integrated List of the same JSNP ID dbSNP ss# dbSNP ss (submitted SNP) number assigned dbSNP rs# dbSNP rs (reference SNP) number assigned 5' Flanking Sequence 5' flanking sequence Observed allele observed 3' Flanking Sequence 3' flanking sequence Offset in Flanking Sequence position of the polymorphism in the flanking sequence Total Length total length of the flanking sequence Accession No. accession No. of the sequence for polymorphism screening Offset in Record position of the polymorphism in the sequence for polymorphism screening Comment Type 1: the polymorphism overlaps with a repetitive sequence 2: the flanking sequence overlaps with a repetitive sequence Gene Symbol gene where the polymorphism is found (information from LocusLink, GenBank and Unigene) JSNP previous ID JSNP previous ID (IDs of IMS-JST104817 to IMS-JST105472 and IMS-JST075266 to IMS-JST075585 are reassigned with ssj IDs) JSNP reference ID JSNP reference ID (where multiple JSNP IDs are assigned to the same polymorphism)

JSNP ID JSNP ID Panel_ID ID of the pool of Japanese individuals where the frequency was examined - JBIC-allele - 752 anonymous unrelated Japanese volunteers - RIKEN-allele - 893 anonymous unrelated Japanese volunteers - POP_102 - 144 unrelated Japanese volunteers with rheumatoid arthritis under informed consent - POP_103 - 16 unrelated Japanese volunteers with adult-onset Still's disease under informed consent - POP_104 - 92 healthy unrelated Japanese volunteers under informed consent - RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteers ( body mass index = 30kg/m2 ) dbSNP ss# dbSNP ss (submitted SNP) number assigned dbSNP rs# dbSNP rs (reference SNP) number assigned allele-1 allele-1 allele-2 allele-2 allele-1 frequency allele-1 frequency allele-2 frequency allele-2 frequency the number of chromosomes examined the number of chromosomes where the frequency was examined (sample size)

JSNP ID JSNP ID In Gene type of gene region where the polymorphism - promoter*1: annotated in GenBank entries - promoter*2: predicted by GENSCAN - promoter*3: putative promoter (1.5kb upstream of the initiation position of mRNA records in the RefSeq) - CDS*1: annotated in GenBank entries either positively or passively - CDS*2: predicted by GENSCAN - CDS*3: extracted by homology search with cDNA - exon*1: annotated in GenBank entries either positively or passively - exon*3: extracted by homology search with mRNA/cDNA/Unigene records - intron*1: annotated in GenBank entries or intervened by Exon*1 and CDS*1 - intron*2: intervened by CDS*2 - intron*3: intervened by exon*3 and CDS*3 - others: surrounding regions of genes Type type of polymorphisms - SNP: single nucleotide polymorphism - IND: insertion/deletion - MIC: microsatelite Frequencies minor allele frequencies in dbSNP; number in brackets means JSNP original allele frequency allele allele observed dbSNP ss# dbSNP ss (submitted SNP) number assigned dbSNP rs# dbSNP rs (reference SNP) number assigned HGVbase-ID ID in HGCbase 5' assay 5' flanking sequence 3' assay 3' flanking sequence Screened Accession accession No. of the sequence for polymorphism screening Screened Position position of the polymorphism in the sequence for polymorphism screening Screened Symbol gene name related to the sequence for polymorphism screening Screened OMIM-ID OMIM ID related to the sequence for polymorphism screening

snp_id ID of JSNP snp_type snp type: SNP or IND (insertion/deletion) 5_flank_seq 5'-flanking sequence of the snp na_var nucleic acids variation 3_flank_seq 3'-flanking sequence of the snp for_primer forward primer sequence for e-PCR back_primer backward primer sequence product_size PCR product size freq_minor minor allele frequency of the snp (-1: no frequency information) from JSNP freq_major major allele frequency of the snp from JSNP chr chromosome number that the snp is mapped chr_start start position of the snp in the chromosome chr_end end position of the snp in the chromosome chr_direct direction of the flanking sequences against the chromosome contig_acc ACC of genomic contig (RefSeq NT) that the snp is mapped contig_start start position of the snp in the genomic contig contig_end end position of the snp in the genomic contig contig_direct direction of the flanking sequences against the genomic contig hit_count number of hit (mapped positions of the snp against genome) gene_na_acc ACC of a gene (RefSeq NM/XM) that the snp is mapped gene_aa_acc ACC of the gene (RefSeq NP/XP) that the snp is mapped symbol symbol of gene that the snp is mapped locus_id ID of gene (LocusLink) that the snp is mapped gene_direct direction of the flanking sequences against the direction of the gene: if the directions of the flanking sequences and of the gene are the same, this is "+"; otherwise "-". str_type gene structure that the snp is mapped: CDS, exon, intron, 5'-UTR, 3'-UTR aa_var amino acids variation codon_var codon variation codon_posi snp postion in the codon dbsnp_rs_id dbSNP rs (reference SNP) number assigned dbsnp_ss_id dbSNP ss (submitted SNP) number assigned

JSNP ID JSNP ID Chromosome Chromosome number Location cytogenetic band Evidence of Location information source of cytogenic band - GenBank "/chromosome" and "/map" - EntrezGene "CHR" and "MAP" - UniGene "CHROMOSOME" and "CYTOBAND" In Gene Type of gene region - promoter*1: Annotated in GenBank entries - promoter*2: Predicted by GENSCAN - promoter*3: Putative promoter (1.5kb upstream of the initiation position of mRNA records in the RefSeq) - CDS*1: Annotated in GenBank entries either positively or passively - CDS*2: Predicted by GENSCAN - CDS*3: Extracted by homology search with cDNA - exon*1: Annotated in GenBank entries either positively or passively - exon*3: Extracted by homology search with mRNA/cDNA/Unigene records - intron*1: Annotated in GenBank entries or intervened by Exon*1 and CDS*1 - intron*2: Intervened by CDS*2 - intron*3: Intervened by exon*3 and CDS*3 - others: surrounding regions of genes Type type of polymorphisms - SNP: single nucleotide polymorphism - IND: insertion/deletion - MIC: microsatelite Frequencies minor allele frequencies in dbSNP, number in brackets means JSNP original allele frequency allele allele observed dbSNP ss# dbSNP ss (submitted SNP) number assigned dbSNP rs# dbSNP rs (reference SNP) number assigned HGVBase-ID ID in HGCbase 5' assay 5' flanking sequence 3' assay 3' flanking sequence Mapping Accession accession No. of the mapped sequence Mapping Position position of the polymorphism in the mapped sequence Mapping Symbol gene name relevant to the mapped sequence Mapping OMIM-ID OMIM ID relevant to the mapped sequence Screened Accession accession No. of the sequence for polymorphism screening Screened Position position of the polymorphism in the sequence for polymorphism screening Screened Symbol gene name relevant to the sequence for polymorphism screening Screened OMIM-ID OMIM ID relevant to the sequence for polymorphism screening

Accession Number Accession number of EST Clone Name Clone name of EST Length Sequence length (bp) GO check_date Date of InterProScan run GO Iprscan Value Link to result of InterProScan GO ID Assigned GO IDs NR blast_date Date of BLAST search (DB: NCBI nr) NR value Result of BLAST search (DB: NCBI nr) NR definition Definition of homologous sequence (DB: NCBI nr) Drosophila blast_date Date of BLAST search (DB: D. melanogaster proteins) Drosophila value Result of BLAST search (DB: D. melanogaster proteins) Drosophila definition Definition of homologous sequence (DB: D. melanogaster proteins) C.elegans blast_date Date of BLAST search (DB: C.elegans proteins) C.elegans value Result of BLAST search (DB: C.elegans proteins) C.elegans definition Definition of homologous sequence (DB: C.elegans proteins) Anopheles blast_date Date of BLAST search (DB: A. gambiae proteins) Anopheles value Result of BLAST search (DB: A. gambiae proteins) Anopheles definition Definition of homologous sequence (DB: Anopheles) Apis blast_date Date of BLAST search (DB: A. mellifera proteins) Apis value Result of BLAST search (DB: A. mellifera proteins) Apis definition Definition of homologous sequence (DB: A. mellifera proteins) Tribolium blast_date Date of BLAST search (DB: T. castaneum proteins) Tribolium value Result of BLAST search (DB: T. castaneum proteins) Tribolium definition Definition of homologous sequence (DB: T. castaneum proteins) Cluster Size Number of sequences in cluster Rep ID Accession number of the representative sequence cDNA library name cDNA library name Sequence Sequence

Rep ID Accession number of the representative EST of each cluster Cluster Size Number of total clones in each cluster an-- Number of identical clones (cDNA library an--) bmmt Number of identical clones (cDNA library bmmt) bmov Number of identical clones (cDNA library bmov) bmte Number of identical clones (cDNA library bmte) BmN- Number of identical clones (cDNA library BmN-) br-- Number of identical clones (cDNA library br--) brP- Number of identical clones (cDNA library brP-) brS- Number of identical clones (cDNA library brS-) caL- Number of identical clones (cDNA library caL-) ce-- Number of identical clones (cDNA library ce--) ceN- Number of identical clones (cDNA library ceN-) cesb Number of identical clones (cDNA library cesb) dpe- Number of identical clones (cDNA library dpe-) e100 Number of identical clones (cDNA library e100) e4 Number of identical clones (cDNA library e4) e96h Number of identical clones (cDNA library e96h) epM- Number of identical clones (cDNA library epM-) epV3 Number of identical clones (cDNA library epV3) F1mg Number of identical clones (cDNA library F1mg) famL Number of identical clones (cDNA library famL) fbf Number of identical clones (cDNA library fbf) fbm Number of identical clones (cDNA library fbm) fbpv Number of identical clones (cDNA library fbpv) fbS2 Number of identical clones (cDNA library fbS2) fcaL Number of identical clones (cDNA library fcaL) fcP8 Number of identical clones (cDNA library fcP8) fe8d Number of identical clones (cDNA library fe8d) ffbm Number of identical clones (cDNA library ffbm) FJsb Number of identical clones (cDNA library FJsb) fmgV Number of identical clones (cDNA library fmgV) fner Number of identical clones (cDNA library fner) ftes Number of identical clones (cDNA library ftes) fufe Number of identical clones (cDNA library fufe) fwgP Number of identical clones (cDNA library fwgP) heS0 Number of identical clones (cDNA library heS0) heS3 Number of identical clones (cDNA library heS3) J150 Number of identical clones (cDNA library J150) JFsb Number of identical clones (cDNA library JFsb) maV3 Number of identical clones (cDNA library maV3) MFB- Number of identical clones (cDNA library MFB-) mg Number of identical clones (cDNA library mg) msgV Number of identical clones (cDNA library msgV) MSV3 Number of identical clones (cDNA library MSV3) mxg- Number of identical clones (cDNA library mxg-) n Number of identical clones (cDNA library n) Nnor Number of identical clones (cDNA library Nnor) NRPG Number of identical clones (cDNA library NRPG) NV02 Number of identical clones (cDNA library NV02) NV06 Number of identical clones (cDNA library NV06) NV12 Number of identical clones (cDNA library NV12) ovS0 Number of identical clones (cDNA library ovS0) ovS3 Number of identical clones (cDNA library ovS3) P5PG Number of identical clones (cDNA library P5PG) pg-- Number of identical clones (cDNA library pg--) phe- Number of identical clones (cDNA library phe-) prgv Number of identical clones (cDNA library prgv) prW- Number of identical clones (cDNA library prW-) ps4M Number of identical clones (cDNA library ps4M) psV3 Number of identical clones (cDNA library psV3) PSV3 Number of identical clones (cDNA library PSV3) tesS Number of identical clones (cDNA library tesS) tesV Number of identical clones (cDNA library tesV) vg4M Number of identical clones (cDNA library vg4M) wd-- Number of identical clones (cDNA library wd--) wdV1 Number of identical clones (cDNA library wdV1) wdV3 Number of identical clones (cDNA library wdV3) ws0 Number of identical clones (cDNA library ws0) ws2 Number of identical clones (cDNA library ws2) ws3 Number of identical clones (cDNA library ws3) wv4 Number of identical clones (cDNA library wv4) swa Number of identical clones (cDNA library swa) swb Number of identical clones (cDNA library swb) swc Number of identical clones (cDNA library swc) swd Number of identical clones (cDNA library swd) swe Number of identical clones (cDNA library swe) swf Number of identical clones (cDNA library swf) swg Number of identical clones (cDNA library swg) swh Number of identical clones (cDNA library swh) swj Number of identical clones (cDNA library swj) swk Number of identical clones (cDNA library swk) swl Number of identical clones (cDNA library swl) swp Number of identical clones (cDNA library swp) BmP Number of identical clones (cDNA library BmP) L1 Number of identical clones (cDNA library L1) L2 Number of identical clones (cDNA library L2) L3 Number of identical clones (cDNA library L3) L4 Number of identical clones (cDNA library L4) L5 Number of identical clones (cDNA library L5) L6 Number of identical clones (cDNA library L6) L7 Number of identical clones (cDNA library L7) L8 Number of identical clones (cDNA library L8) L9 Number of identical clones (cDNA library L9) L10 Number of identical clones (cDNA library L10) L11 Number of identical clones (cDNA library L11) L12 Number of identical clones (cDNA library L12) L13 Number of identical clones (cDNA library L13) L14 Number of identical clones (cDNA library L14) L15 Number of identical clones (cDNA library L15) L16 Number of identical clones (cDNA library L16) Other Number of identical clones (other cDNA libraries)

Rep ID Accession number of the representative EST ORF Name Name of ORF Frame Number of Frame ORF Number Number of ORF Threshold Threshold of sequence length (including the stop codon) Length Sequence length (bp) Sequence Amino acid Sequence

Rep ID Accession number of the representative EST ORF Name Name of ORF CRC64 Value of CRC64 in each sequence Length Sequence length (bp) Analysis Database/Program used for analysis Signature Accession Signature accession Signature Description Signature description Start location Start location of Motif Stop location Stop location of Motif Score E-value of matching score to the functional site sequence Status Status of match to the functional site sequence (T: match) InterPro accession Assigned InterPro ID InterPro description Description of assigned InterPro ID GO terms Assigned GO terms

Registered library name Registered name of the partial cDNA library Library synonym Another name for cDNA library (original name) Local library name Local library name Strain/Race Strain/race Organ/Tissue Organ / tissue Developmental stage Developmental stage Sex Sex Vector Vector Cloning sites Cloning site Sequence direction Direction of sequencing Accession number Range of accession numbers Clone name Naming rule of clones Note Note

D number Unique identifier of the KEGG DRUG entry. Classification Shown when the drug is Mixture, Crude or Formula. Name The generic name and selected trade names of the drug. Component Component Formula The molecular formula of the drug structure. Exact mass The exact mass of the drug structure. Mol weight The molecular weight of the drug structure. Structural formula Chemical structural formula. (Simple search only) Sequence Sequence data when the drug is a peptide or a polyketide. Sequence type Sequence type (NRP, PK, Peptide). Source Biological source when the drug is derived from a natural product. Upper DGroup Upper DGroup. Remark This field contains Therapeutic category, ATC code, and also identical entries in the COMPOUND database. Efficacy Efficacy and activity of the drug. Disease The desease healed by the drug. Comment Free text comment. Target Target information of the drug with appropriate links to human genes and KEGG Orthology. Metabolism Information about drug metabolizing enzyme and transporter. Interaction Other interaction information, including CYP induction and inhibition, genomic biomarkers, etc. Other DBs Links to outside databases. KCF data The KCF (KEGG Chemical Function) representation of the chemical structure can be displayed here. It contains the KEGG atom type information for use in chemical structure comparisons.

E number Unique identifier of the KEGG ENVIRON entry. Name Name of the natural product. Category Category (Crude drug, Essential oil or Medicinal herb). Component Chemical components and corresponding C/D numbers. Source Biological source with links to NCBI taxonomy IDs. Remark D number of the same crude drug, etc. when available. Comment Free text comment. Other DBs Links to outside databases.

H number Unique identifier of the KEGG DISEASE entry. Name Disease names including alternative names. Sub Group Sub group of the disease Super Group Super group of the disease [H number] Description A brief summary of the disease. Category The category of the disease. Network The network whici contains the disease Gene Known disease genes with links to the KEGG GENES and KO databases. Pathogen Known pathogens with links to the KEGG GENOME and VGENOME databases. Env factor Known other environmental factors with links to the KEGG COMPOUND and other databases. Carcinogen Known carcinogens with links to the KEGG COMPOUND and other databases. Drug Typical therapeutic drugs with links to the KEGG DRUG database. Comment Free text comment. Other DBs Links to outside databases. Reference Reference information.

DG number Unique identifier of the KEGG DGROUP entry. Classification Shown when the group is "Chemical". Name Name of the DGroup. Stem Stem of drugs in the DGroup. Structural formula Chemical structural formula. (Simple search only) Member List of drugs and D numbers in the DGroup. Upper DGroup Upper DGroup. Remark ATC code. Comment Free text comment.

N number Unique identifier of the KEGG NETWORK entry (Network). Name Name of the molecular network. Definition Definition of the molecular network. Definition expressed by ID Above definition is expressed by element ID. Upper group Maps contains the molecular network. Type Molecular network type Disease Related disease. Gene Genes contained in the molecular network. Variant Variants contained in the molecular network. Metabolite Metabolites contained in the molecular network. Perturbant Perturbants contained in the molecular network. Reference Reference information.

nt number Unique identifier of the KEGG NETWORK entry (Network Map). Name Name of the molecular network. Map name Name of the network map. Disease Related disease. Other DBs Links to outside databases. Member Molecular networks contained in the map.

Variant ID Unique identifier of the KEGG VARIANT entry. Name Name of the variant. Gene Gene name Organism Organism Variation Variation names and links to outside databases. Map Molocular network maps which contain the variant. Network Molocular network which contain the variant. Reference Reference information.

Category Category of the dataset Title Title of the dataset Description Description of the dataset Sequence data file Name of the fasta file Data file (CSV) Name of the CSV file Data file (TogoDB) Name of the dataset on Simple search website (TogoDB)

ACCESSION_NO DDBJ accession number of the full-length cDNA clone. All the clones in the database were registered in DDBJ. CLONE_ID ID number assigned to each full-length cDNA clone BELONG Initial of the research institute where the clone was sequenced. (R: RIKEN, F: FAIS) CLONE_NAME Name of the full-length cDNA clone CLUSTER_ID Cluster ID of the full-length cDNA clone. Cluster IDs were numbered serially. LENGTH Length of the full-length cDNA sequence POLYA_CUT_LENGTH Length of the full-length cDNA sequence excluding the poly(A) region SEQ_QUALITY Ratio of non-N residues contained in the full-length cDNA sequence POLYA_CUT_SEQ_QUALITY Ratio of non-N residues contained in the full-length cDNA sequence excluding the poly(A) region SEQ_ACCURACY Sequence accuracy calculated as the average of accuracies of individual bases after a sequencing run. LIBRARY Information about the full-length cDNA library, such as tissues which the library derived from and their treatment conditions.

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BAC_ACCESSION_NO Accession number of the mapped BAC contigs CHROMOSOME Chromosome number of the mapped BAC contigs BAC_START_POS Alignment start position on the mapped BAC contigs BAC_END_POS Alignment end position on the mapped BAC contigs CDNA_START_POS Alignment start position on the mapped cDNA clone CDNA_END_POS Alignment end position on the mapped cDNA clone STRAND Strand direction of the mapped cDNA clone TU_ID ID of the mapped TU (Transcriptional Unit)

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BAC_ACCESSION_NO Accession number of the mapped BAC contigs CHROMOSOME Chromosome number of the mapped BAC contigs BAC_START_POS Exon start position on the mapped BAC contigs BAC_END_POS Exon end position on the mapped BAC contigs CDNA_START_POS Exon start position on the mapped cDNA clone CDNA_END_POS Exon end position on the mapped cDNA clone STRAND Strand direction of the mapped cDNA clone TU_ID ID of the mapped TU (Transcriptional Unit)

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone HIT_NUMBER Number of the sites where the cDNA clones were mapped PSEUDOMOLECULE Name of the mapped pseudomolecule CHROMOSOME Chromosome number of the mapped pseudomolecule CHR_START_POS Alignment start position on the mapped pseudomolecule CHR_END_POS Alignment end position on the mapped pseudomolecule CDNA_START_POS Alignment start position on the mapped cDNA clone CDNA_END_POS Alignment end position on the mapped cDNA clone STRAND Strand direction of the mapped cDNA clone TU_ID ID of the mapped TU (Transcriptional Unit)

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone HIT_NUMBER Number of the sites where the cDNA clones were mapped PSEUDOMOLECULE Accession number of the mapped pseudomolecule CHROMOSOME Chromosome number of the mapped pseudomolecule CHR_START_POS Exon start position on the mapped pseudomolecule CHR_END_POS Exon end position on the mapped pseudomolecule CDNA_START_POS Exon start position on the mapped cDNA clone CDNA_END_POS Exon end position on the mapped cDNA clone STRAND Strand direction of the mapped cDNA clone TU_ID ID of the mapped TU (Transcriptional Unit)

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the blast search result ACCESSION Accession number of the GenBank entry DEFINITION Definition of the GenBank clone DIVISION GenBank division SCORE Score in the blastn search result EXPECT Expect value in the blastn search result IDENTITIES Identities in the blastn search result STRAND1_1 Strand direction of the subject sequence STRAND1_2 Strand direction of the query sequence

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the blastx search result ACCESSION Accession number of the GenBank entry DEFINITION Definition of the GenBank clone DIVISION GenBank division SCORE Score in the blastx search result EXPECT Expect value in the blastx search result IDENTITIES Identities in the blastx search result FRAME Reading frame of the full-length cDNA clone

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BLAST_TYPE Type of BLAST program (blastn or blastx) HIT_ACCESSION Accession number of the GenBank entry DIVISION GenBank division DEFINITION Definition of the GenBank clone RANK Ranking in the blast search result SCORE Score in the blast search result EXPECT Expect value in the blast search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BLAST_TYPE Type of BLAST program (blastn or blastx) HIT_ACCESSION Accession number of the GenBank entry DIVISION GenBank division DEFINITION Definition of the GenBank clone RANK Ranking in the blast search result SCORE Score in the blast search result EXPECT Expect value in the blast search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BAC_ACCESSION_NO Accession number of the GenBank entry DEFINITION Definition in the GenBank entry EXPECT Expect value in the blastn search result SCORE Score in the blastn search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone INDICA_ACCESSION Accession number of the GenBank entry DEFINITION Definition in the GenBank entry EXPECT Expect value in the blastn search result SCORE Score in the blastn search result STRAND Strand direction of the cDNA clone

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone ARRAY_ELEMENT Element number of the G-Array probe PROBE_ACCESSION Accession number of the G-Array probe PROBE_CLONE_NAME Clone name of the G-Array probe EXPECT Expect value in the blastn search result SCORE Score in the blastn search result

ACCESSION_NO Accession number of the full-length cDNA clone FULL_CLONE_NAME Name of the full-length cDNA clone TOS_NAME Name of the Tos17 clone BAC_ACCESSION_NO Accession number of the mapped BAC clone TOS_INSERT_POSITION Insert position of the Tos17 clone on the BAC contigs cDNA_START_POSITION Mapping start position of the cDNA clone on the BAC contigs cDNA_END_POSITION Mapping end position of the cDNA clone on the BAC contigs

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone HIT_NO Ranking in the sigscan search result SIGNAL_NAME Name of the signal element SIGNAL_TYPE Signal type LOCATION Signal position STRAND Strand direction of the query cDNA sequence SIGNAL_SEQ Signal sequence SIGNAL_ID Signal element ID in PLACE

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone FRAME_NO Frame number START_POSITION Start position of the longest ORF STOP_POSITION End position of the longest ORF LENGTH Length of the longest ORF OCCUPATION Ratio of the ORF length to the cDNA sequence length

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone MIPS_CODE MIPS code in the Arabidopsis thaliana database DEFINITION Definition of CDS in the Arabidopsis thaliana database EXPECT Expect value in the blastp search result SCORE Score in the blastp search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the blastx search result PIR_ACCESSION Accession number in the PIR protein database DEFINITION Definition of the protein in the PIR protein database EXPECT Expect value in the blastx search result SCORE Score in the blastx search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the blastx search result DEFINITION Definition of the protein in the Swiss-Prot database ENTRY_NAME Name of the protein in the Swiss-Prot database EXPECT Expect value in the blastx search result SCORE Score in the blastx search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the blastx search result UNIPROT ID UniProt ID DEFINITION Definition of the protein in the UniProt database EXPECT Expect value in the blastx search result SCORE Score in the blastx search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone INTERPRO_ID ID of the motif in the InterPro database INTERPRO_NAME Name of the motif in the InterPro database METHOD Motif search program ACCESSION_ID Accession number of the motif SHORT_NAME Short name of the motif LOCATION Location of the motif EXPECT Expect value in the search result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the search result ACCESSION Accession number of the motif in the Blocks Database DESCRIPTION Description of the motif in the Blocks Database STRENGTH Strength in the BLIMPS result SCORE Score in the BLIMPS result RF Reading frame (Always 0 since the sequence is in amino acids) POSITION Position of the motif MOTIF_SEQ Amino acid sequence of the motif MOTIF_LENGTH Length of the amino acid sequence of the motif

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone GO_ACCESSION Accession number of the GO term

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone GO_ACCESSION Accession number of the GO term

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone GO_ACCESSION Accession number of the GO term

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone COUNT Number of transmembrane regions WAY Direction of 5' end

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RANK Ranking in the PSORT prediction result TARGET Target organelle of the predicted signal sequence CERTAINTY Certainty in the PSORT prediction result SCORE Score in the WoLF PSORT prediction result

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone RPD_ID ID of the protein in the Rice Proteome Database that is homologous to the clone SCORE Score in the blastn search result COVERAGE Query coverage between the protein in the Rice Proteome Database and the clone

ACCESSION Accession number of the full-length cDNA clone CLONE_ID ID of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone CLUSTER_ID Cluster ID BELONG Initial of the research institute where the clone was sequenced. (R: RIKEN, F: FAIS) SEQUENCE Nucleotide sequence

ACCESSION_NO Accession number of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone BELONG Initial of the research institute where the clone was sequenced. (R: RIKEN, F: FAIS) SEQ_DATA Sequence after trimming TRIM_TOP Length of the sequence trimmed from 5' end TRIM_END Length of the sequence trimmed from 3' end TRIM_LENGTH Length of the sequence after trimming

ACCESSION Accession number of the full-length cDNA clone CLONE_ID ID of the full-length cDNA clone CLONE_NAME Name of the full-length cDNA clone CLUSTER_ID Cluster ID BELONG Initial of the research institute where the clone was sequenced. (R: RIKEN, F: FAIS) SEQUENCE Amino acid sequence

CLONE_NAME Name of the full-length cDNA clone 3'EST_NAME 3' EST name 5'EST_NAME 5' EST name

3'EST_NAME 3' EST name SEQUENCE 3' EST sequence

5'EST_NAME 5' EST name SEQUENCE 5' EST sequence

LIGANDBOX_ID ID in LigandBox SINGLE "ture" if the entry is extacted as single conformer, else "false". SOURCE Source of this compound SOURCE_ID ID in the source MOLECULAR_FORMULA Molecular formula MOLECULAR_WEIGHT Molecular weight MOLECULAR_CHARGE Molecular charge NUM_OF_DONOR Number of hydrogen bond donors NUM_OF_ACCEPTOR Number of hydrogen bond acceptors NUM_OF_CHIRAL_ATOMS Number of chiral atoms TPSA Topological Polar Surface Area HOMO Highest Occupied Molecular Orbital energy LUMO Lowest Unoccupied Molecular Orbital energy LOGP Partition coefficient LOGS Solubility MOL2_FILE URL of mol2 file for the entry

LIGANDBOX_ID ID in LigandBox SINGLE "TRUE" if the entry is extacted as single conformer, else "FALSE". SOURCE Source of this compound SOURCE_ID ID in the source MOLECULAR_FORMULA Molecular formula MOLECULAR_WEIGHT Molecular weight MOLECULAR_CHARGE Molecular charge NUM_OF_DONOR Number of hydrogen bond donors NUM_OF_ACCEPTOR Number of hydrogen bond acceptors NUM_OF_CHIRAL_ATOMS Number of chiral atoms TPSA Topological Polar Surface Area HOMO Highest Occupied Molecular Orbital energy LUMO Lowest Unoccupied Molecular Orbital energy LOGP Partition coefficient LOGS Solubility MOL2_FILE URL of mol2 file for the entry

LIGANDBOX_ID ID in LigandBox SINGLE "true" if the entry is extacted as single conformer, else "false". SOURCE Source of this compound SOURCE_ID ID in the source MOLECULAR_FORMULA Molecular formula MOLECULAR_WEIGHT Molecular weight MOLECULAR_CHARGE Molecular charge NUM_OF_DONOR Number of hydrogen bond donors NUM_OF_ACCEPTOR Number of hydrogen bond acceptors NUM_OF_CHIRAL_ATOMS Number of chiral atoms TPSA Topological Polar Surface Area HOMO Highest Occupied Molecular Orbital energy LUMO Lowest Unoccupied Molecular Orbital energy LOGP Partition coefficient LOGS Solubility MOL2_FILE URL of mol2 file for the entry

LIGANDBOX_ID ID in LigandBox SINGLE "TRUE" if the entry is extacted as single conformer, else "FALSE". SOURCE Source of this compound SOURCE_ID ID in the source MOLECULAR_FORMULA Molecular formula MOLECULAR_WEIGHT Molecular weight MOLECULAR_CHARGE Molecular charge NUM_OF_DONOR Number of hydrogen bond donors NUM_OF_ACCEPTOR Number of hydrogen bond acceptors NUM_OF_CHIRAL_ATOMS Number of chiral atoms TPSA Topological Polar Surface Area HOMO Highest Occupied Molecular Orbital energy LUMO Lowest Unoccupied Molecular Orbital energy LOGP Partition coefficient LOGS Solubility MOL2_FILE URL of mol2 file for the entry

Surface form The word itself Left-context ID MeCab internal ID for left context (see http://taku910.github.io/mecab/dic.html) Right-context ID MeCab internal ID for right context (see http://taku910.github.io/mecab/dic.html) Cost The cost for the likelihood of the word to appear in a sentence (smaller, more likely) POS Part of speech POS subcategory 1 POS subcategory 1 POS subcategory 2 POS subcategory 2 POS subcategory 3 POS subcategory 3 Conjugation type Conjugation type Conjugation form Conjugation form Base form Corresponding headword in the JST thesaurus Reading('Furigana') Reading of the headword. When Headword Flag is ’V’, it may be different from the reading of the surface form. Pronunciation Automatically generated from Reading Source dictionary It is fixed as 'Thesaurus2015'. ID in Source dictionary ID in JST Thesaurus J-GLOBAL ID ID in J-GLOBAL Headword Flag ・C: The word's surface form is the same as the headword in JST Thesaurus (or corresponding hankaku form) ・V: Otherwise Category code Category code of science fields in JST Thesaurus Common word flag 1 ・1: There is an entry (or entries) for the surface form in IPA dictionary ・0: There are no entries for the surface in IPA dictionary Common word flag 2 Based on "IPA dictionary analysis results": ・When the value of Common word flag １ is 1, the value of this flag is the part of speech for the IPA dictionary analysis result. ・When the value of Common word flag １ is 0: - UNKNOWN_1: if the result is one unknown word - UNKNOWN_2: if the result is multiple tokens including unknown word - MULTI_WORD: if the result is multiple tokens in IPA dictionary IPA dictionary analysis results Results of the morphological analysis with the original IPA dictionary (and the dictionary with IPA dictionary entries where zenkaku alphanumeric characters and symbols are converted into corresponding hankaku characters). If the result is devided into multiple tokens, it is whitespace-separated. It is not manually corrected.

Surface form The word itself Left-context ID MeCab internal ID for left context (see http://taku910.github.io/mecab/dic.html) Right-context ID MeCab internal ID for right context (see http://taku910.github.io/mecab/dic.html) Cost The cost for the likelihood of the word to appear in a sentence (smaller, more likely) POS Part of speech POS subcategory 1 POS subcategory 1 POS subcategory 2 POS subcategory 2 POS subcategory 3 POS subcategory 3 Conjugation type Conjugation type Conjugation form Conjugation form Base form Same as the surface form Reading('Furigana') (empty) Pronunciation (empty) Source dictionary It is fixed as 'MeSH'. ID in Source dictionary MeSH UID J-GLOBAL ID ID in J-GLOBAL Headword Flag It is fixed as 'C'. Category code Category code of science fields in JST Thesaurus Common word flag 1 ・1: There is an entry (or entries) for the surface form in IPA dictionary ・0: There are no entries for the surface in IPA dictionary Common word flag 2 Based on "IPA dictionary analysis results": ・When the value of Common word flag １ is 1, the value of this flag is the part of speech for the IPA dictionary analysis result. ・When the value of Common word flag １ is 0: - UNKNOWN_1: if the result is one unknown word - UNKNOWN_2: if the result is multiple tokens including unknown word - MULTI_WORD: if the result is multiple tokens in IPA dictionary IPA dictionary analysis results Results of the morphological analysis with the original IPA dictionary (and the dictionary with IPA dictionary entries where zenkaku alphanumeric characters and symbols are converted into corresponding hankaku characters). If the result is devided into multiple tokens, it is whitespace-separated. It is not manually corrected.

Surface form The word itself Left-context ID MeCab internal ID for left context (see http://taku910.github.io/mecab/dic.html) Right-context ID MeCab internal ID for right context (see http://taku910.github.io/mecab/dic.html) Cost The cost for the likelihood of the word to appear in a sentence (smaller, more likely) POS Part of speech POS subcategory 1 POS subcategory 1 POS subcategory 2 POS subcategory 2 POS subcategory 3 POS subcategory 3 Conjugation type Conjugation type Conjugation form Conjugation form Base form Same as the surface form Reading('Furigana') (empty) Pronunciation (empty) Source dictionary It is fixed as 'Nikkaji'. ID in Source dictionary MeSH UID J-GLOBAL ID ID in J-GLOBAL Headword Flag It is fixed as 'C'. Category code Category code of science fields in JST Thesaurus Common word flag 1 ・1: There is an entry (or entries) for the surface form in IPA dictionary ・0: There are no entries for the surface in IPA dictionary Common word flag 2 Based on "IPA dictionary analysis results": ・When the value of Common word flag １ is 1, the value of this flag is the part of speech for the IPA dictionary analysis result. ・When the value of Common word flag １ is 0: - UNKNOWN_1: if the result is one unknown word - UNKNOWN_2: if the result is multiple tokens including unknown word - MULTI_WORD: if the result is multiple tokens in IPA dictionary IPA dictionary analysis results Results of the morphological analysis with the original IPA dictionary (and the dictionary with IPA dictionary entries where zenkaku alphanumeric characters and symbols are converted into corresponding hankaku characters). If the result is devided into multiple tokens, it is whitespace-separated. It is not manually corrected.

Sample Set ID Sample set ID Title Sample set name Description Describes important concepts for interpreting data, such as experiment purposes and relevancy between samples. Authors Author Reference Related reference information Comment Comment Experimental Conditions Link to Experimental Conditions (only in Simple search)

Sample Set ID Sample Set ID ("Sample Set ID" and "Sample ID" are merged into "ID" in the Simple search.) Sample ID Sample ID ("Sample Set ID" and "Sample ID" are merged into "ID" in the Simple search.) Title Sample name Organism - Scientific Name Scientific name Organism - ID Classification ID of the organism. Compound - ID Compound ID Compound - Source Information about the availability of the reagent: the company name and catalog id. Preparation Growing methods, conditions, particular processing, sampling portions, sampling methods, and preparation methods for reagents Comment Comment Analytical Method IDs Link to Analytical Method (M) (only in Simple search)

Sample Set ID Sample Set ID ("Sample Set ID", "Analytical Method ID" and "Sample ID" are merged into "ID" in the Simple search.) Analytical Method ID Analysis method ID ("Sample Set ID", "Analytical Method ID" and "Sample ID" are merged into "ID" in the Simple search.) Title Analysis method name Analytical Method Details ID Detailed analysis information ID (MS) applied. ("Analytical Method Details ID" and "Sample ID" are merged into "ID" in the Simple search.) Sample Amount An amount of sample used. This information is necessary for normalizing quantitative data to compare with other samples. Comment Comment Data Analysis IDs Link to Data Analysis (D) (only in Simple search)

Sample Set ID Sample Set ID ("Sample Set ID", "Data Analysis ID", "Sample ID" and "Analytical Method ID" are merged into "ID" in the Simple search.) Data Analysis ID Data analysis method ID ("Sample Set ID", "Data Analysis ID", "Sample ID" and "Analytical Method ID" are merged into "ID" in the Simple search.) Title Data analysis method name Data Analysis Details ID Detailed data analysis method information ID (DS) applied. ("Data Analysis Details ID" and "Sample ID" are merged into "ID" in the Simple search.) Recommended decimal places of mass Number of significant figures. Comment Comment

Sample Set ID Sample Set ID ("Sample Set ID" and "Analytical Method Details ID" are merged into "ID" in the Simple search.) Analytical Method Details ID Detailed analysis information ID ("Sample Set ID" and "Analytical Method Details ID" are merged into "ID" in the Simple search.) Title Detailed analysis information name Instrument Instrument name and vendor name Instrument Type Instrument type Ionization Method Ionization method Ion Mode Distinction of positive analysis and negative analysis Description Details about methods of instrumental analysis. Describes all details regarding analytical instruments and analysis conditions. Comment_of_details Comment

Sample Set ID Sample Set ID ("Sample Set ID" and "Data Analysis Details ID" are merged into "ID" in the Simple search.) Data Analysis Details ID Detailed analysis method information ID ("Sample Set ID" and "Data Analysis Details ID" are merged into "ID" in the Simple search.) Title Detailed analysis method information name Description Describes all details regarding data analysis methods such as software programs used and the parameters adopted. Comment_of_details Comment

Sample Set ID Sample Set ID ("Sample Set ID" and "Annotation Method Details ID" are merged into "ID" in the Simple search.) Annotation Method Details ID Annotation method ID ("Sample Set ID" and "Annotation Method Details ID" are merged into "ID" in the Simple search.) Title Annotation method name Description Describes details regarding annotation methods. Describes standards by which annotation has been assigned. Comment_of_details Comment

Sample Set ID Sample Set ID ("Sample Set ID" and "Sample Preparation ID" are merged into "ID" in the Simple search.) Sample Preparation ID The sample preparation details ID ("Sample Set ID" and "Sample Preparation ID" are merged into "ID" in the Simple search.) Title Sample preparation name Description Details about sample preparation. In the case of biological samples, for example, details of growth conditions and drug treatments are described. Descriptions that depend on analytical methods should not be included here, and they should be included in the details of analytical methods (MS). Comment_of_details Comment

Data Analysis ID Data analysis method ID Sample Set ID Sample Set ID (Not shown in the Simple search) Sample Set Sample set name Sample ID Sample ID (Not shown in the Simple search) Sample Sample name Analytical Method ID Analytical Method ID (Not shown in the Simple search) Sample Amount An amount of sample used. Sample Comment Sample comment Analytical Method Details ID Detailed analysis information ID (MS) applied. (Not shown in the Simple search) Analytical Method Details Detailed analysis information name Data Analysis Details ID Detailed analysis method information ID (Not shown in the Simple search) Data Analysis Details Detailed analysis method information name Recommended decimal places of mass Number of significant figures. Annotation Method ID Annotation method ID (Not shown in the Simple search) Annotation Method Annotation method name Sample Preparation ID The sample preparation details ID (Not shown in the Simple search) Sample Preparation Sample preparation name

brc/nbrc/ Metadata of strains in NBRC. brc/jcm/ Metadata of strains in JCM.

ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes). ontology/meo/meo_fma_mapping.ttl An ontology mapping files that was mapped between MEO and FMA. ontology/msv/msv.ttl An ontology for describing several states of sampling environment for metagenome analyses. ontology/mdbv/mdbv.rdf A vocabulary for describing data schema in MicrobeDB.jp version 2. ontology/mgfo/mgfo.ttl An ontology for describing the gene function category that is used in MBGD. ontology/pdo/pdo.owl An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection. ontology/csso/csso.owl An ontology for describing clinical signs and symptoms. ontology/mpo/mpo.ttl An ontology for describing microbial phenotypes. ontology/mccv/mccv.ttl Structured controlled vocabulary for describing meta information of microbial culture collection maintained in biological resource centers. ontology/taxonomy/taxonomy.ttl Modified NCBI Taxonomy ontology for describing taxonomic relationships of organisms. ontology/insdc/nucleotide.ttl A vocabulary for describing metadata of INSDC entries.

sra/metadata/meo_mapping/ The MEO annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/metadata/msv_mapping/ The MSV annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/metadata/host_taxonomy_mapping/ The NCBI Taxonomy annotation results of host organisms of microbes for 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/metadata/sra_description/ The metadata descriptions of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/sra/function/mbgd/ The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/sra/function/mgfo/ The MBGD ortholog functional composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/sra/function/ko/ The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/sra/function/pathway/ The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/sra/taxonomy/ The taxonomic composition of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA. sra/analysis/env/function/mbgd/ The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category. sra/analysis/env/function/mgfo/ The MBGD ortholog function composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category. sra/analysis/env/function/ko/ The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category. sra/analysis/env/function/pathway/ The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category. sra/analysis/env/taxonomy/meta16s/ The taxonomic composition of 16S rRNA gene-based amplicon sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category. sra/analysis/env/taxonomy/metagenome/ The taxonomic composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.

ncbi/bioproject/ The RDF files of metadata of NCBI BioProject. ncbi/biosample/ The RDF files of metadata of NCBI BioSample with the annotations of MEO, MSV, and NCBI Taxonomy. ncbi/pubmed/ The RDF files of metadata of PubMed. ncbi/assembly/ The RDF files of metadata of Assembly Reports in NCBI Assembly.

Protein Category Protein Category Protein Name Protein Name Mouse Genomic Loci Chromosome region of the mouse gene locus Human Genomic Loci Chromosome region of the human gene locus Genbank Accession # Genbank Accession Number of the coding region in the mRNA MGI MGI ID of the gene Mouse Embryo Age in days of mouse embryo (In simple search, it shows the link to mouse embryo image page) Antibody Antibody to stain the target protein Validation Validation result (medium or high)

Protein Name Protein Name Antibody Name Antibody Name Producer / Vender Producer / Vender Catalog # Catalog # Immunization Species Immunization Species Clonality Clonality(monoclonal or polyclonal) Fixative Fixative Hyaluronidase / Chondroitinase Treatment Hyaluronidase / Chondroitinase Treatment Acid Treatment Acid Treatment Validation Score Validation result (medium or high) Validation Detail of validation result

plant Line name sub Individual number date observed date image image file name comment_j comment Japanese comment_e comment English phenotype keyword of phenotype

id Phenotype ID category_j Category in Japanese category_e Category in English description_j Phenotype name in Japanese description_e Phenotype name in English comment comment

id Phenotype ID name Strain Name

Sequence Name Sequence name Line Name Line name Accession Accession number

Chromosome Chromosome number Position Position of Tos17 insertion Direction Direction of Tos17 E-value E-value Line name Line name Sequence Name Name of Tos17 flanking sequence

Nikkaji Number Identifier of Chemical Substances in Nikkaji InChI IUPAC International Chemical Identifier InChIKey IUPAC International Chemical Identifier Key

Medals oligonucleic drug ID Medals oligonucleic drug ID (issued by MEDALS) ATC Classification ATC classification Product Name Product name Synonims Synonims Country Country Company Company Phase AD: Approved I-III: PhaseI-III R: Rejected Type Nucleotide type Adaptation Diseases Adaptation diseases Target Molecule Target molecule Remarks Remarks Nucleic Acid Sequence Nucleic acid sequence Source Source DrugBank DrugBank ID TargetProtein - UniProt TargetProtein - UniProt ID TargetProtein - PDB TargetProtein - PDB ID

COMPOUND_NAME Compound name COMPOUND_ABBREVIATION Abbreviated compound name COMPOUND_NO Number assigned to each compound. Numbers are not in serial order. Human - in vitro Gene expression data of in vitro tests with human liver cells (Link to a zip file which contains multiple CEL files) Rat - in vitro Gene expression data of in vitro tests with rat liver cells (Link to a zip file which contains multiple CEL files) Rat - in vivo - Liver - Single Gene expression data of single-dose in vivo tests with rat liver (Link to a zip file which contains multiple CEL files) Rat - in vivo - Liver - Repeat Gene expression data of repeat-dose in vivo tests with rat liver (Link to a zip file which contains multiple CEL files) Rat - in vivo - Kidney - Single Gene expression data of single-dose in vivo tests with rat kidney (Link to a zip file which contains multiple CEL files) Rat - in vivo - Kidney - Repeat Gene expression data of repeat-dose in vivo tests with rat kidney (Link to a zip file which contains multiple CEL files) Pathological items (Liver) Pathological findings and slide images of in vivo tests with rat liver (Link to "Pathological items", "Pathological images" and "CEL file attributes") Pathological items (Kidney) Pathological findings and slide images of in vivo tests with rat kidney (Link to "Pathological items", "Pathological images" and "CEL file attributes")

BARCODE Bar-code assigned to each GeneChip in order to indentify. Bar-code matches CEL file name without extension. ARR_DESIGN In the project, HG-U133_Plus_2 was used for human and Rat230_2 was used for rat. EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual/sample within a group. IDs are in single digit. ORGAN Organ evaluated in tests. Liver or Kidney. MATERIAL_ID ID assigned to each tissue section which was used to acquire gene expression data. IDs are in a single letter. COMPOUND_NAME Compound name COMPOUND_ABBREVIATION Abbreviated compound name COMPOUND_NO Number assigned to each compound. Numbers are not in serial order. SPECIES Species EXP_TEST_TYPE Type of test. In vivo test or in vitro test. SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SEX_TYPE Gender. Male or Female. STRAIN_TYPE Rat strain used with in vivo tests ADMINISTRATION_ROUTE_TYPE Administration route ANIMAL_AGE(week) Age of animal (weeks). Only rats at 6 weeks of age were used. SACRIFICE_PERIOD Sampling time or period. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High.

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each sample within a group. IDs are in single digit. COMPOUND_NAME Compound name SPECIES Species SEX_TYPE Gender. Male or Female. SACRIFICE_PERIOD Duration of exposure on in vitro test. DOSE Concentration DOSE_UNIT Unit of concentration DOSE_LEVEL Exposure level. The ascending order of the levels is Control, Low, Middle, High. BARCODE Link to "CEL file attributes" CELL_VIABILITY Link to "Cell viability"

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each sample within a group. IDs are in single digit. COMPOUND_NAME Compound name SPECIES Species SEX_TYPE Gender. Male or Female. SACRIFICE_PERIOD Duration of exposure on in vitro test. DOSE Concentration DOSE_UNIT Unit of concentration DOSE_LEVEL Exposure level. The ascending order of the levels is Control, Low, Middle, High. DNA(%) Relative survival rate calculated from DNA content. LDH(%) Relative survival rate calculated from the activity value of lactate dehydrogenase which is leaked in the culture supernatant.

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SEX_TYPE Gender. Male or Female. STRAIN_TYPE Rat strain used with in vivo tests ADMINISTRATION_ROUTE_TYPE Administration route ANIMAL_AGE(week) Age of animal (weeks). Only rats at 6 weeks of age were used. SACRIFICE_PERIOD Sampling time or period on in vivo test. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. BARCODE (Liver) Link to "CEL file attributes (Liver)" BARCODE (Kidney) Link to "CEL file attributes (Kidney)" HEMATOLOGY Link to "Hematology" BIOCHEMISTRY Link to "Biochemistry" ORGAN_WEIGHT Link to "Organ weight" BODY_WEIGHT Link to "Body weight" FOOD_CONSUMPTION Link to "Food consumption" PATHOLOGY (Liver) Link to "Pathological items (Liver)" PATHOLOGY (Kidney) Link to "Pathological items (Kidney)" PATHOLOGICAL_IMAGE (Liver) Link to "Pathological images (Liver)" PATHOLOGICAL_IMAGE (Kidney) Link to "Pathological images (Kidney)"

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SEX_TYPE Gender. Male or Female. STRAIN_TYPE Rat strain used with in vivo tests ADMINISTRATION_ROUTE_TYPE Administration route ANIMAL_AGE(week) Age of animal (weeks). Only rats at 6 weeks of age were used. SACRIFICE_PERIOD Sampling time or period on in vivo test. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. TERMINAL_BW(g) Terminal body weight LIVER(g) The weight of the liver KIDNEY_TOTAL(g) The total weight of the kidneys KIDNEY_R(g) The weight of the right kidney KIDNEY_L(g) The weight of the left kidney

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SACRIFICE_PERIOD Sampling time or period on in vivo test. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. RBC(x10_4/ul) red blood cell count Hb(g/dL) hemoglobin Ht(%) hematocrit value MCV(fL) mean corpuscular volume MCH(pg) mean corpuscular hemoglobin MCHC(%) mean corpuscular hemoglobin concentration Ret(%) reticulocyte Plat(x10_4/uL) platelet count WBC(x10_2/uL) white blood cell count Neu(%) neutrophil Eos(%) eosinophil Bas(%) basophil Mono(%) monocyte Lym(%) lymphocyte PT(s) prothrombin time APTT(s) activated partial thromboplastin time Fbg(mg/dL) fibrinogen

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SACRIFICE_PERIOD Sampling time or period on in vivo test. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. ALP(IU/L) alkaline phosphatase TC(mg/dL) total cholesterol TG(mg/dL) triglyceride PL(mg/dL) phospholipid TBIL(mg/dL) total bilirubin DBIL(mg/dL) direct bilirubin GLC(mg/dL) glucose BUN(mg/dL) blood urea nitrogen CRE(mg/dL) creatinine Na(meq/L) sodium K(meq/L) potassium Cl(meq/L) chlorine Ca(mg/dL) calcium IP(mg/dL) inorganic phosphorus TP(g/dL) total protein RALB(g/dL) albumin A/G albumin globulin ratio AST(IU/L) aspartate aminotransferase ALT(IU/L) alanine aminotransferase LDH(IU/L) lactate dehydrogenase GTP(IU/L) γ-glutamyltranspeptidase

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. SACRIFICE_PERIOD Sampling time or period on in vivo test. PROGRESS_TIME Measurement date of body weight. The unit is day. The day when the administration was started is counted as day 1. BODY_WEIGHT Body weight of the rat on the day of PROGRESS_TIME. The unit is gram.

EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. SACRIFICE_PERIOD Sampling time or period on in vivo test. PROGRESS_TIME Measurement date of food consumption. The unit is day. The day when the administration was started is counted as day 1. FC_AMOUNT The amount of daily food intake. The unit is gram per day (g/day).

BARCODE Bar-code assigned to each GeneChip in order to indentify. Bar-code matches CEL file name without extension. Data with the value "No ChipData" don't have a corresponding CEL file since the microarray gene expression analysis wasn't performed. EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. SACRIFICE_PERIOD Sampling time or period on in vivo test. ORGAN Organ evaluated in tests. Liver or Kidney. FINDING_TYPE Pathological findings. TOPOGRAPHY_TYPE Region of the organ where the pathological changes were found. GRADE_TYPE Magnitude of pathological changes. The ascending order of the magnitude is P(present), minimal, slight, moderate, severe. SP_FLG The flag shows whether the lesion occurred spontaneously. The flag value is "1" if the lesion occurred spontaneously. PATHOLOGICAL_IMAGE Link to "Pathological images"

BARCODE Bar-code assigned to each GeneChip in order to indentify. Bar-code matches CEL file name without extension. Data with the value "No ChipData" don't have a corresponding CEL file since the microarray gene expression analysis wasn't performed. ARR_DESIGN In the project, HG-U133_Plus_2 was used for human and Rat230_2 was used for rat. EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000. GROUP_ID ID assigned to each group which can be indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. ORGAN Organ evaluated in tests. Liver or Kidney. MATERIAL_ID ID assigned to each tissue section which was used to acquire gene expression data. IDs are in a single letter. COMPOUND_NAME Compound name COMPOUND_ABBREVIATION Abbreviated compound name COMPOUND_NO Number assigned to each compound. Numbers are not in serial order. SPECIES Species EXP_TEST_TYPE Type of test. In vivo test or in vitro test. SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. SEX_TYPE Gender. Male or Female. STRAIN_TYPE Rat strain used with in vivo tests ADMINISTRATION_ROUTE_TYPE Administration route ANIMAL_AGE(week) Age of animal (weeks). Only rats at 6 weeks of age were used. SACRIFICE_PERIOD Sampling time or period. DOSE Dose DOSE_UNIT Unit of dose DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High. Organ Weight TERMINAL_BW(g) terminal body weight LIVER(g) the weight of the liver KIDNEY_TOTAL(g) the total weight of the kidneys KIDNEY_R(g) the weight of the right kidney KIDNEY_L(g) the weight of the left kidney Hematology RBC(x10_4/ul) red blood cell count Hb(g/dL) hemoglobin Ht(%) hematocrit value MCV(fL) mean corpuscular volume MCH(pg) mean corpuscular hemoglobin MCHC(%) mean corpuscular hemoglobin concentration Ret(%) reticulocyte Plat(x10_4/uL) platelet count WBC(x10_2/uL) white blood cell count Neu(%) neutrophil Eos(%) eosinophil Bas(%) basophil Mono(%) monocyte Lym(%) lymphocyte PT(s) prothrombin time APTT(s) activated partial thromboplastin time Fbg(mg/dL) fibrinogen Biochemistry ALP(IU/L) alkaline phosphatase TC(mg/dL) total cholesterol TG(mg/dL) triglyceride PL(mg/dL) phospholipid TBIL(mg/dL) total bilirubin DBIL(mg/dL) direct bilirubin GLC(mg/dL) glucose BUN(mg/dL) blood urea nitrogen CRE(mg/dL) creatinine Na(meq/L) sodium K(meq/L) potassium Cl(meq/L) chlorine Ca(mg/dL) calcium IP(mg/dL) inorganic phosphorus TP(g/dL) total protein RALB(g/dL) albumin A/G albumin globulin ratio AST(IU/L) aspartate aminotransferase ALT(IU/L) alanine aminotransferase LDH(IU/L) lactate dehydrogenase GTP(IU/L) γ-glutamyltranspeptidase Cell viability DNA(%) Relative survival rate calculated from DNA content. LDH(%) Relative survival rate calculated from the activity value of lactate dehydrogenase which is leaked in the culture supernatant.

EXP_ID ID assigned to each test which is defined mainly as a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are #0040 or larger. GROUP_ID ID assigned to each group which is defined mainly as a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit. COMPOUND_NAME Compound name ORGAN Organs evaluated in tests. Liver or Kidney. FILE_LOCATION FTP server path to the pathological images. CAPTURE_NO/NO_OF_SAMPLE(n/n) The sequence number of scanned images with the total number. 1/2 means that 2 glass slides were scanned for an organ and that the image is the first one. SPECIES Species SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test. ADMINISTRATION_ROUTE_TYPE Administration route ANIMAL_AGE(week) Age of animal (weeks). SACRIFICE_PERIOD Sampling time or period on in vivo test. DOSE Dose DOSE_UNIT Unit of dose

GI number NCBI GI number of Amino Acid sequence RefSeq ID NCBI Reference Sequence ID Chr Chromosome number or genomic ID Start Position Start Position Stop Position Stop Position Cluster (Kingdom) Cluster ID (rank: Kingdom) Cluster (Phylum) Cluster ID (rank: Phylum) Cluster (No rank 1) Cluster ID (rank: No rank 1) Cluster (No rank 2) Cluster ID (rank: No rank 2) Cluster (No rank 3) Cluster ID (rank: No rank 3) Cluster (No rank 4) Cluster ID (rank: No rank 4) Cluster (No rank 5) Cluster ID (rank: No rank 5) Cluster (No rank 6) Cluster ID (rank: No rank 6) Cluster (No rank 7) Cluster ID (rank: No rank 7) Cluster (No rank 8) Cluster ID (rank: No rank 8) Cluster (No rank 9) Cluster ID (rank: No rank 9) Cluster (No rank 10) Cluster ID (rank: No rank 10) Cluster (Class) Cluster ID (rank: Class) Cluster (No rank 11) Cluster ID (rank: No rank 11) Cluster (Subclass) Cluster ID (rank: Subclass) Cluster (No rank 12) Cluster ID (rank: No rank 12) Cluster (Order) Cluster ID (rank: Order) Cluster (Family) Cluster ID (rank: Family) Cluster (No rank 13) Cluster ID (rank: No rank 13) Cluster (Subfamily) Cluster ID (rank: Subfamily) Cluster (No rank 14) Cluster ID (rank: No rank 14) Cluster (Tribe) Cluster ID (rank: Tribe) Cluster (Subtribe) Cluster ID (rank: Subtribe) Cluster (Genus) Cluster ID (rank: Genus) Cluster (Subgenus) Cluster ID (rank: Subgenus) Cluster (Species) Cluster ID (rank: Species) Cluster (Subspecies) Cluster ID (rank: Subspecies) Cluster (Forma) Cluster ID (rank: Forma) Cluster (No rank 15) Cluster ID (rank: No rank 15) Annotation Annotation of protein Organism Organism AA sequence Amino acid sequence

Cluster ID The cluster ID is composed of a Taxonomy ID and a serial number beginning with “0”. For instance, “cluster ID: 33090.0” means the protein belongs to the cluster ranked 0th among the clusters in the “taxon: 33090”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins affiliated with the Cluster Supercluster Next supercluster Subcluster Next subcluster

Taxonomy name NCBI Taxonomy name Taxonomy ID NCBI Taxonomy ID Taxonomy rank NCBI Taxonomy rank Number of clusters Number of clusters affiliated with the Taxon Number of proteins Number of proteins affiliated with the Taxon Higher taxon Next suprageneric taxon Lower taxon Next infrageneric taxon

GI number NCBI GI number of Amino Acid sequence RefSeq ID NCBI Reference Sequence ID Chr Chromosome number or genomic ID Start Position Start Position Stop Position Stop Position Cluster (Phylum) Cluster ID (rank: Phylum) Cluster (Class) Cluster ID (rank: Class) Cluster (Order) Cluster ID (rank: Order) Cluster (No rank 1) Cluster ID (rank: No rank 1) Cluster (Family) Cluster ID (rank: Family) Cluster (Genus) Cluster ID (rank: Genus) Cluster (No rank 2) Cluster ID (rank: No rank 2) Cluster (Species) Cluster ID (rank: Species) Cluster (No rank 3) Cluster ID (rank: No rank 3) Cluster (Subspecies) Cluster ID (rank: Subspecies) Cluster (No rank 4) Cluster ID (rank: No rank 4) Annotation Annotation of protein Organism Organism AA sequence Amino acid sequence

Cluster ID The cluster ID is composed of a Taxonomy ID and a serial number beginning with “0”. For instance, “cluster ID: 33090.0” means the protein belongs to the cluster ranked 0th among the clusters in the “taxon: 33090”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins affiliated with the Cluster Supercluster Next supercluster Subcluster Next subcluster

Taxonomy name NCBI Taxonomy name Taxonomy ID NCBI Taxonomy ID Taxonomy rank NCBI Taxonomy rank Number of clusters Number of clusters affiliated with the Taxon Number of proteins Number of proteins affiliated with the Taxon Higher taxon Next suprageneric taxon Lower taxon Next infrageneric taxon

Gene name (Link to Image list) Gene name (Link to "Image list" in simple search.) Single-cell PCR data (+ describes cells expressing the gene.) "+" indicates a cell co-expressing each gene and a neural-specific marker gene EF1. Mapping on FACS profile PCR data plotting onto the FACS profile, in which cells are sorted by DNA content (Hoechst33342) and cell size (CalceinAM). Blue dots indicate the "+"cells. The FACS profile image is displayed when you click "FACS Profile" in simple search. In the downloaded data, its file name is shown.

Gene name (Link to Image list) Gene name (Link to a image list in simple search.) Accession GenBank accession number (Link to NCBI in simple search.) Adult (ISH) Image of in situ hybridization of adult planarians. (The image is displayed in simple search. In the downloaded data, its file name is shown.) Adult (Ab) Image of whole-mount immunostaining of intact planarians. (The image is displayed in simple search. In the downloaded data, its file name is shown.) Regeneration 1 day (Ab) Image of immunostaining at 1 day after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.) Regeneration 3 days (Ab) Image of immunostaining at 3 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.) Regeneration 5 days (Ab) Image of immunostaining at 5 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.) Regeneration 7 days (Ab) Image of immunostaining at 7 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.)

Identifier Identifier Accession number Accession number Date (operation) author Date (operation) author Description Description (regulation, gene, transacting factor, etc.) Keywords Keywords Species Species Sequence Sequence of the cis-acting regulatory DNA element. For the cis-acting elements the following symbols were used as codes representing A, G, C or T. B: C, G or T D: A, G or T H: A, C or T K: G or T M: A or C N: A, C, G or T R: A or G S: C or G V: A, C or G W: A or T Y: C or T (Mar. 31, 1997)

Identifier Identifier Authors Authors Title Title Literature data Literature data Criteria Criteria (DNase I footprinting study / Chemical modifications / Gel retardation assay / homology / other) PubMed PubMed ID GenBank DDBJ/EMBL/GenBank accession number

ID Identifier AC Accession number DT Date (operation) author DE Description (regulation, gene, transacting factor, etc.) KW Keywords OS Species RA Authors RT Title RL Literature data RC Criteria (DNase I footprinting study / Chemical modifications / Gel retardation assay / homology / other) RD External Database (MEDLINE number or DDBJ/EMBL/GenBank accession number) SQ Sequence of the cis-acting regulatory DNA element. For the cis-acting elements the following symbols were used as codes representing A, G, C or T. B: C, G or T D: A, G or T H: A, C or T K: G or T M: A or C N: A, C, G or T R: A or G S: C or G V: A, C or G W: A or T Y: C or T (Mar. 31, 1997) XX Data item delimiter

Old data ID Identifier in old data (r01.1 or earlier : Identifier, r02.0 or later : "unknown") ID Identifier (r01.1 or earlier : Name, r02.0 or later : Identifier) Sequence Sequence of the cis-acting regulatory DNA element. For the cis-acting elements the following symbols were used as codes representing A, G, C or T. B: C, G or T D: A, G or T H: A, C or T K: G or T M: A or C N: A, C, G or T R: A or G S: C or G V: A, C or G W: A or T Y: C or T (Mar. 31, 1997) Sequence length Sequence length Accession number Accession number

PocketIndex Internal ID for this binding site PDB_ID PDB ID for the protein HET_Code HET code for the ligand ChainID ID for the chain where the binding site is HET_Res.No. Residue sequence number of the ligand ResLength Length of residue sequence of the site Atoms Num of atoms of the ligand MolName Molecular name of the site EC EC ID for the site CATH CATH ID for the site SCOPe SCOPe ID for the site UniProt UniProt ID for the site UniRef50 UniRef50 cluster ID for the site (when it is analysed) GO1 Gene ontology to indicate molecular function of the site GO2 Gene ontology to indicate molecular function of the site GO3 Gene ontology to indicate molecular function of the site

PocketIndex Internal ID for this binding site PDB_ID PDB ID for the protein HET_Code HET code for the ligand ChainID ID for the chain where the binding site is ResLength Length of residue sequence of the site Atoms Num of atoms of the ligand MolName Molecular name of the site EC EC ID for the site CATH CATH ID for the site SCOPe SCOPe ID for the site UniProt UniProt ID for the site UniRef50 UniRef50 cluster ID for the site (when it is analysed) GO1 Gene ontology to indicate molecular function of the site GO2 Gene ontology to indicate molecular function of the site GO3 Gene ontology to indicate molecular function of the site

Q:PocketIndex Internal ID for query site Ｔ:PocketIndex Internal ID for target site Q:PDB_ID PDB ID for query site T:PDB_ID PDB ID for target site Q:HET_Code HED code for query site T:HET_Code HED code for target site Q:ChainID ID for the chain where the query site is T:ChainID ID for the chain where the target site is Q:Res.No. Residence number for the amino acid where the query site is T:Res.No. Residence number for the amino acid where the target site is Cosine Cosine similarity with physicochemical and geometric properties AlignedLength Length of amino acid alignment RMSD Root Mean Square Deviation TM-score Template modeling score of protein structure Pval P-Value of similarity AminoIdentity Amino acid match rate MolName Molecular name of the site EC EC ID for the site CATH CATH ID for the site SCOPe SCOPe ID for the site UniProt UniProt ID for the site UniRef50 UniRef50 cluster ID for the site (when it is analysed) GO1 Gene ontology to indicate molecular function of the site GO2 Gene ontology to indicate molecular function of the site GO3 Gene ontology to indicate molecular function of the site AlignedResidues Amino acid alignment result

Q:PocketIndex Internal ID for query site Ｔ:PocketIndex Internal ID for target site Q:PDB_ID PDB ID for query site T:PDB_ID PDB ID for target site Q:HET_Code HED code for query site T:HET_Code HED code for target site Q:ChainID ID for the chain where the query site is T:ChainID ID for the chain where the target site is Q:Res.No. Residence number for the amino acid where the query site is T:Res.No. Residence number for the amino acid where the target site is Cosine Cosine similarity with physicochemical and geometric properties AlignedLength Length of amino acid alignment RMSD Root Mean Square Deviation TM-score Template modeling score of protein structure Pval P-Value of similarity AminoIdentity Amino acid match rate MolName Molecular name of the site EC EC ID for the site CATH CATH ID for the site SCOPe SCOPe ID for the site UniProt UniProt ID for the site UniRef50 UniRef50 cluster ID for the site (when it is analysed) GO1 Gene ontology to indicate molecular function of the site GO2 Gene ontology to indicate molecular function of the site GO3 Gene ontology to indicate molecular function of the site AlignedResidues Amino acid alignment result

ID Internal ID for this ligand HET_Code HET Code Link Link to tables in Drug Search (only in simple search) ChEMBL_ID ChEMBL ID PrefName Preferred name HeavyAtoms Number of heavy atoms FullMWT Full molocular weight Alogp Value of ALogP HBA Number of H-bond acceptors HBD Number of H-bond donors RotatableBonds Number of ratatable bonds PSA Polar surface area ATC_Level1 Classification in ATC level1 ATC_Level2 Classification in ATC level2 ATC_Level3 Classification in ATC level3 ATC_Level4 Classification in ATC level4

PocketIndex Internal ID for this binding site PDB_ID PDB ID for the protein HET_Code HET code for the ligand ChainID ID for the chain where the binding site is Res.No. Residence number for the amino acid where the binding site is MolName Molecular name of the protein UniProt UniProt ID for the protein UniRef50 UniRef50 claster ID for the protein (when it is analysed) EC EC ID for the protein CATH CATH ID for the protein SCOPe SCOPe scope for the ligand

PocketIndex Internal ID for this binding site PDB_ID PDB ID for the protein HET_Code HET code for the ligand ChainID ID for the chain where the binding site is Res.No. Residence number for the amino acid where the binding site is MolName Molecular name of the protein UniProt UniProt ID for the protein UniRef50 UniRef50 cluster ID for the protein (when it is analysed) EC EC ID for the protein CATH CATH ID for the protein SCOPe SCOPe scope for the ligand

HET_Code HET Code for the ligand SimilarPockets Internal id of site binding the ligand JaccardIndex(MACCS) Jaccard Index between ligand and target site (with MACCS) JaccardIndex(FP2) Jaccard Index between ligand and target site (with FP2) InChi_Key InChIKey of binding molocular CanonicalSmiles Canonical SMILES of binding molocular

Q:PocketIndex Internal ID for query site Ｔ:PocketIndex Internal ID for target site Q:PDB_ID PDB ID for query site T:PDB_ID PDB ID for target site Q:HET_Code HED code for query site T:HET_Code HED code for target site Q:ChainID ID for the chain where the query site is T:ChainID ID for the chain where the target site is Q:Res.No. Residence number for the amino acid where the query site is T:Res.No. Residence number for the amino acid where the target site is AlignedLength Length of amino acid alignment RMSD Root Mean Square Deviation AminoIdentity Amino acid match rate Q:MolName Molecular name of the query site T:MolName Molecular name of the target site Q:EC EC ID for the query site T:EC EC ID for the target site Q:CATH CATH ID for the query site T:CATH CATH ID for the target site Q:SCOPe SCOPe ID for the query site T:SCOPe SCOPe ID for the target site Q:UniProt UniProt ID for the query site T:UniProt UniProt ID for the target site Q:UniRef50 UniRef50 cluster ID for the query site (when it is analysed) T:UniRef50 UniRef50 cluster ID for the target site (when it is analysed) EC_Df Different or not between query and target site in EC ID CATH_Df Different or not between query and target site in CATH ID SCOPe_Df Different or not between query and target site in SCOPe ID ChEMBL_Assay Assay data in ChEMBL or none AlignedResidues Amino acid alignment result

Q:PocketIndex Internal ID for query site Ｔ:PocketIndex Internal ID for target site Q:PDB_ID PDB ID for query site T:PDB_ID PDB ID for target site Q:HET_Code HED code for query site T:HET_Code HED code for target site Q:ChainID ID for the chain where the query site is T:ChainID ID for the chain where the target site is Q:Res.No. Residence number for the amino acid where the query site is T:Res.No. Residence number for the amino acid where the target site is AlignedLength Length of amino acid alignment RMSD Root Mean Square Deviation AminoIdentity Amino acid match rate Q:MolName Molecular name of the query site T:MolName Molecular name of the target site Q:EC EC ID for the query site T:EC EC ID for the target site Q:CATH CATH ID for the query site T:CATH CATH ID for the target site Q:SCOPe SCOPe ID for the query site T:SCOPe SCOPe ID for the target site Q:UniProt UniProt ID for the query site T:UniProt UniProt ID for the target site Q:UniRef50 UniRef50 cluster ID for the query site (when it is analysed) T:UniRef50 UniRef50 cluster ID for the target site (when it is analysed) EC_Df Different or not between query and target site in EC ID CATH_Df Different or not between query and target site in CATH ID SCOPe_Df Different or not between query and target site in SCOPe ID ChEMBL_Assay Assay data in ChEMBL or none AlignedResidues Amino acid alignment result

PSCID ID of this data Classification The six digit numbers (from left to right) are, respectively, 1st: the number of components of motion for the coupled domain motion 2nd: the number for the independent domain motion 3rd: the number for the coupled local motion 4th: the number for the independent local motion 5th: the number of domains exhibiting the burying ligand motion 6th: the number of domains with ligand molecules situated on the protein surface. Protein name Protein name FreeID PDB ID of ligand-free form BoundID PDB ID of ligand-bound form Ligands Ligand name(PDB) EC Enzyme commission number Distance The distance between the active site annotated in Catalytic Site Atlas (CSA) and the ligand-binding sites

PSCID ID of this data Classification The six digit numbers (from left to right) are, respectively, 1st: the number of components of motion for the coupled domain motion 2nd: the number for the independent domain motion 3rd: the number for the coupled local motion 4th: the number for the independent local motion 5th: the number of domains exhibiting the burying ligand motion 6th: the number of domains with ligand molecules situated on the protein surface. Protein name Protein name FreeID PDB ID of ligand-free form BoundID PDB ID of ligand-bound form Ligands Ligand name(PDB) EC Enzyme commission number Distance The distance between the active site annotated in Catalytic Site Atlas (CSA) and the ligand-binding sites Component No Component Number Type of motion Type of motion Ligand binding Type of ligand binding Type of coupled motion Type of coupled motion Order-disorder transition Whether the open form contains the disordered structure. ("Yes" or space) RMSD The root-mean-square displacement of a component of motion calculated for the domain motions Mean displacement The mean displacement of a component of motion calculated for the local motions C.C. The correlation coefficient between the displacement vector predicted by the linear response theory and the one observed in the crystal structures Crystal packing Whether the change in the crystal environment is coupled with the structural change. ("Coupled" or space) Fixed segment Fixed segment Moving segment Moving segment Disorder The number of disordered residues Helix/coil The number of residues exhibiting the alpha-helix to coil transition Open state Distinction between the open state and the closed state required for examining the influence of the crystal environment H-bonds/ligand The number of hydrogen-bonds with ligands (observed in the proteins classified in "Buried Ligand") H-bonds/water The number of hydrogen-bonds with water (observed in the proteins classified in "Buried Ligand") H-bonds/protein The number of hydrogen-bonds with proteins (observed in the proteins classified in "Buried Ligand")

id ID number of QTL QTL/Gene Name of QTL Major category Major category of quantitative character Category of object character Category of object character Character Character Marker Type of marker No. of marker for position determination Number of the markers used for position determination Chr Chromosome number Genome start QTL start position on the genome Genome end QTL end position on the genome Mapping method Mapping method Population Population of plants No. of plants Number of plants LOD LOD score Parent A Parent A Parent B Parent B Direction (Parent) Direction (Parent) a) Physical Marker of physical mapping b) Fine1; interval Flanking marker of fine mapping A b) Fine2; interval Flanking marker of fine mapping B b) Fine3; co-segregated Co-segregated marker of fine mapping c) Interval1; interval Flanking marker of interval mapping A c) Interval2; interval Flanking marker of interval mapping B c) Interval3; co-segregated Co-segregated marker of interval mapping d) Co-segregated Co-segregated marker Explained variance Explained variance Additive effect Additive effect Year Year the reference was published Reference source Search method of the reference. Journals were searched within the following websites. - Jsa (Jstage) - Pha (PubMed, HighWire) - RGN (Rice Genetics Newsletter) Reference no. Number assigned to the reference serially within each reference source Reference Reference Reference location URL of the reference

Probe no Probe number Probe ID Probe ID TU ID ID of the TU (Transcriptional Unit) Microarray Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database Accession Gene Accession number of probe 5'end Accession Gene Accession number of probe 5'end 3'end Accession Gene Accession number of probe 3'end Gene name Gene name Probe name Probe name Annotation Probe Annotation 5'probe sequence Sequence of probe 5'end 3'probe sequence Sequence of probe 3'end

Experiment no Experiment number Experiment ID String connected by a '_' between "Research ID", "Round", "Group no" of "Control ID" data and "Group no" of "Target ID" data. Microarray Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database Control ID Control Data, correspondence to column of "Sample ID" on the redii_inaho_sample table. Target ID Target Data, correspondence to column of "Sample ID" on the redii_inaho_sample table. Control dye Control dye Target dye Target dye Experimenter User name Institute Organization Experimental category1 Experimental category 1 Experimental category2 Experimental category 2 Experimental category3 Experimental category 3 Experimental category4 Experimental category 4 Keyword Experimental keyword Method Method Experiment Date 1 Experiment date 1 Glass ID 1 Array glass ID 1 Glass Production Date 1 Array glass production date 1 Spotter No 1 Spot number 1 Pen Set ID 1 Pen set ID 1 Glass Batch ID 1 Array glass batch 1 Experiment Date 2 Experiment date 2 Glass ID 2 Array glass ID 2 Glass Production Date 2 Array glass production date 2 Spotter No 2 Spot number 2 Pen Set ID 2 Pen set ID 2 Glass Batch ID 2 Array glass batch 2

Sample ID Sample ID Microarray Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database Experiment ID Original experimental ID. String connected by a '_' between "Research ID", "Round" and "Group no". Organism Organism Subspecies Subspecies Cultivar Cultivar, Line Developmental Stage Developmental stage Tissue Tissue Mutant Mutant Transgenic Transgenic

Microarray Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database Experiment no Experiment number Spot ID Spot ID Probe no Probe number Probe name Probe name Expression value Expression value (log ratio)

Species Species of object Experimental Method Experimantal method of collecting expression data. Kind of ID Kind of ID Gene Expression (classificated in 10 organs) Gene expression data classified in 10 organs. Gene Expression (classificated in 10 organs) DOI DOI of gene expression data classificated in 10 organs. Gene Expression (classificated in 40 organs) Gene expression data classified in 40 organs. Gene Expression (classificated in 40 organs) DOI DOI of gene expression data classificated in 40 organs. Gene Expression (by FANTOM5 CAGE) CAGE data collected by FANTOM5. Gene Expression (by FANTOM5 CAGE) DOI DOI of CAGE data collected by FANTOM5. Sample Classification Table Classification table of each tissue. Sample Classification Table DOI DOI of classification table of each tissue. Sample Annotation Information of sample annotation Sample Annotation DOI DOI of information of sample annotation. Tissue Specificity (calculated by ROKU) Tissue specificity calculated by ROKU method. Tissue Specificity (calculated by ROKU) DOI DOI of tissue specificity calculated by ROKU method.

ID In GeneChip data and RNA-Seq data, Probe set ID by Affymetrix and NCBI RefSeq ID respectively. score Entropy score. When this score is smaller, specificity of the gene is higher. v[tissue ID in RefEx]_[name of tissue] For each tissue, 1: specific high expression, -1: specific low expression, 0: others

NCBI_GeneID NCBI Entrez Gene ID NCBI_UnigeneID NCBI Unigene ID NCBI_RefSeqID NCBI RefSeq ID Affymetrix_probesetID Affymetrix probeset ID organism Organism

Description (RefEx refined) Tissue name 10 groups ID of each tissue classified in 10 organs. 40 groups ID of each tissue classified in 40 organs. GSM_# IDs of all samples used in experiments of each tissue. SINGLE Data on Single-End RNA-Seq PAIRED Data on Pair-End RNA-Seq

CAGE FANTOM5 Original Order Order defined in FANTOM5 Alphabetical Uniq Order by developmental, primary cells Alphabetical order RefEx Tissue Class10 ID of each tissue classified in 10 organs. RefEx Tissue Class40 ID of each tissue classified in 40 organs. Cell Class Class of cell based on its property. Tissue Class Class of tissue based on its property. Description (RefEx refined) Additional information on samples provided by RefEx. FANTOM5 URL URL for information on samples provided by FANTOM5. Description (FANTOM5) Additional information on samples provided by FANTOM5. GeneChip Accession GEO accession of sample Title Sample name Sample Type Type of sample Taxonomy Organism Channels The number of kind of fluorescent pigments in Microarray. Platform GEO accession of experimental platform Series GEO accession of series the sample belongs in. Supplementary Types Formats of available raw data file Supplementary Links URL for raw data file SRA Accession SRA accession Contact Contact about data Release Date Release date of data

Chrom. No. Chromosome number Position in a YAC physical map (cM) Position in a YAC physical map (genetic distance, cM) Marker name Marker name Type of marker Type of marker. Polymorphism between Nipponbare and Kasalath were revealed by STS, CAPS, or dCAPS. NP indicates that no polymorphism was detected between Nipponbare and Kasalath. Enzyme Restriction enzymes used for CAPS and dCAPS to detect polymorphism between Nipponbare and Kasalath. No digestion is needed for STS markers. Amplified band size (bp) Amplified band size in Nipponbare (bp) 5' primer sequence 5' primer sequence 3' primer sequence 3' primer sequence Mapping population Mapping population Position Chromosomal location of each marker is shown by either the RFLP marker co-segregated or the interval of flanking RFLP markers on the previously reported linkage map (Harushima et al. 1998 Genetices 148: 479-494, Lin et al.1998 Theor Appl Genet 96: 997-1003). Comment Comment Image file name 1 Image file name 1 of gel electrophoresis Image file name 2 Image file name 2 of gel electrophoresis Image file name 3 Image file name 3 of gel electrophoresis Image file name 4 Image file name 4 of gel electrophoresis

Chrom. No. Chromosome number (UN: Chromosome unknown) YAC Clones Number of YAC clones YAC Contigs Number of YAC contigs Total Length of YAC Contigs (Mb) Total length of YAC contigs (Mb) Coverage (%) Coverage (%) = Total length (Mb) of YAC contigs / ( genetic length of chromosome (cM) x 430 (Mb) / 1530.4 (cM) ) x 100 EST Sites Number of EST sites Ave EST Density (EST/100 kb) Average EST density (EST/100 kb) = Number of ESTs / total length of YAC contigs Contig Image File Image file name of chromosomal distribution

Anchor Genetic markers used for YAC landing Chrom. No. Chromosome number Position (cM) Genetic distance (cM) EST Clone EST Clone (sites) name DDBJ Acc FW DDBJ accession of the EST clone (Forward sequence) DDBJ Acc RV DDBJ accession of the EST clone (Reverse sequence) Positive YACs Positive YAC names PCR Primer PCR primer name Amplified Band Size Amplified PCR band size (kb) Ann T Annealing temperature (℃) 5'-Primer Sequence Primer sequence (5' primer, each 20 bases) 3'-Primer Sequence Primer sequence (3' primer, each 20 bases) Map Image File Image file name of the rice transcript map

Chrom. No. Number of chromosome (In Simple search site, the chromosome number link to the site of "Detailed information of DNA markers", and the image file name link to the map image.) No. of callus cDNA clones Number of callus cDNA clones No. of root cDNA clones Number of root cDNA clones No. of random genomic clones Number of random genomic clones No. of NotI-linking clones Number of NotI-linking clones No. of YAC end clones Number of YAC end clones No. of telomere-associated clones Number of telomere-associated clones No. of RAPD markers Number of RAPD markers No. of STS markers Number of STS markers No. of wheat clones Number of wheat clones No. of other clones Number of other clones Total marker number Total marker number Total length in error detection off mode Total length in Kosambi map function by error detection off mode of MAPMAKER/EXP Total length in error detection on mode Total length in Kosambi map function by error detection on mode of MAPMAKER/EXP Difference between error detection on and off mode (cM) Difference between error detection on and off mode (cM) Difference between error detection on and off mode (%) Difference between error detection on and off mode (%) No. of candidate errors by MAPMAKER/EXP Number of the candidate errors shown by MAPMAKER/EXP 3.0 Total number of observed genotypes The total number of the observed genotypes to calculate the map Average number of observed genotypes per marker An avarege of the number of the observed genotypes per marker

Chrom. No. Chromosome number Two-point distance (cM) The two-point distances to the previous markers (cM) Position (cM) Marker position in the chromosome (cM) Locus name Locus name DDBJ accession No. DDBJ accession number(s) of the marker sequence Restriction enzyme Names of restriction enzymes to detect the polymorphism between Nipponbare and Kasalath Nipponbare band size (kb) Southern band size of Nipponbare (kb) Kasalath band size (kb) Southern band size of Kasalath (kb) Probe size (kb) Probe size Vector Cloning vector Cloning site Cloning site Special primers or restriction enzymes for NotI-linking clone Special primer set or restriction enzyme set for the preparation of NotI-linking marker RAPD primer sequence 1 RAPD marker primer sequence 1 RAPD primer sequence 2 RAPD marker primer sequence 2 PCR protocol for RAPD and STS markers PCR protocol of RAPD and STS markers Image file name Southern image file name

Chrom. No. Chromosome number Floating marker Floating marker. "F" in this column indicates that the segregation data of the locus did not show any recombination to the loci with the different positions. If "F" is indicated in the column, the minimum position is shown in column "position" and the maximum position is shown in column "max". Position The genetic distance of the locus from the short arm end. If "F" is indicated in "Floating marker" column, the minimum position is shown in this column. Max If "F" is indicated in "Floating marker" column, the maximum position is shown in this column. Marker name Marker name: The "Marker name" corresponds to the "Real name" in "Detailed information of DNA markers". Accession 5'_1 The DDBJ sequence accession number for 5' end of insert fragment that was used as a probe. Accession 5'_2 If there are two accession numbers for 5' end, another number is shown in this column. Accession 3' The DDBJ sequence accession number for 3' end

Chrom. No. Chromosome number Locus name Locus name Real name If the polymorphism is detected at multiple locations, the locus name of marker that match the original sequence information is referred to as "Real name". The "Real name" corresponds to the "Marker name" in ""High-density linkage map information". Restriction enzyme Names of restriction enzymes to detect the polymorphism between Nipponbare and Kasalath Nipponbare band size (kb) Southern band size of Nipponbare (kb) Kasalath band size (kb) Southern band size of Kasalath (kb) Probe size (kb) Probe size Vector Cloning vector Cloning site Cloning site Special primers or restriction enzymes for NotI-linking clone Special primer set or restriction enzyme set for the preparation of NotI-linking marker Primer sequence 1 Primer sequence 1 of marker Primer sequence 2 Primer sequence 2 of marker PCR protocol PCR protocol for markers Image file name Parental Southern image file name

Chrom. No. Chromosome number Genotype data The link to genotypical data for all segregants (186 individuals) on a simple search site Linkage order The link to marker information in order of the linkage map on a simple search site Map image file The link to rice high-density linkage maps on a simple search site

Chrom. No. Chromosome number Floating marker Floating marker "F" in this column indicates that the segregation data of the locus did not show any recombinations to those of the loci with the different positions. If "F" is indicated in this column, the minimum position is shown in "Position" column, and the maximum position is shown in "Max" column. Position The position of the locus from the short arm end. If "F" is indicated in "Floating marker" column, this column is shown the minimum position. Max If "F" is indicated in "Floating marker" column, this column is shown the maximum position Arm Chromosome arm was confirmed in strains of telo-torisomy, by markers used to determine the position of the centromere on linkage map Locus name Locus name Image file name Parental Southern image file name Accession DDBJ accession number of the marker Accession 2 If marker has two accession numbers, another number is shown in this column Orignal clone name The original name of the clone Protein Name of the most similar protein appearing in PIR database R48.0 and SWISS-PROT R33 Organism Organism of the most similar protein appearing in PIR database R48.0 and SWISS-PROT R33 Score Bits score of the most similar protein appering in PIR database R48.0 and SWISS-PROT R33

Chrom. No. Chromosome number Isozyme locus Isozyme locus Enzyme name Enzyme name cDNA locus 1 cDNA locus 1 Position 1 Position 1 cDNA locus 2 cDNA locus 2 Position 2 Position 2 cDNA locus 3 cDNA locus 3 Position 3 Position 3 cDNA locus 4 cDNA locus 4 Position 4 Position 4

Chrom. No. Chromosome number Locus Locus name Genetic code Genetic code by MAPMAKER

Chrom. No. Chromosome number Order Linkage order Markers Marker name Distance The genetic distance to the next marker (cM) Genotypes The genotypical number that was observed per each marker in mapping population. codom : Codominant marker +/- : Dominant marker

Chrom. No. Chromosome number Region Region number Physical map image The file name of rice physical map First marker First DNA marker Distance of first marker (cM) Distance of the first marker from the top of each chromosome (cM) Last marker Last DNA marker Distance of last marker (cM) Distance of the last marker from the top of each chromosome (cM)

Chrom. No. Chromosome number Region Region number Physical map image The file name of rice physical map Order Linkage order Marker Marker name Distance (cM) The genetic distance from the previous marker (cM) YAC clone1 YAC clone 1 The YAC name followed by "c" shows that the YAC is a chimera. YAC clone2 YAC clone 2 YAC clone3 YAC clone 3 YAC clone4 YAC clone 4 YAC clone5 YAC clone 5 YAC clone6 YAC clone 6 YAC clone7 YAC clone 7 YAC clone8 YAC clone 8 YAC clone9 YAC clone 9 YAC clone10 YAC clone 10 YAC clone11 YAC clone 11 YAC clone12 YAC clone 12 YAC clone13 YAC clone 13 YAC clone14 YAC clone 14 YAC clone15 YAC clone 15 YAC clone16 YAC clone 16 YAC clone17 YAC clone 17 YAC clone18 YAC clone 18 YAC clone19 YAC clone 19 YAC clone20 YAC clone 20 YAC clone21 YAC clone 21 YAC clone22 YAC clone 22 YAC clone23 YAC clone 23 YAC clone24 YAC clone 24 YAC clone25 YAC clone 25 YAC clone26 YAC clone 26 YAC clone27 YAC clone 27 YAC clone28 YAC clone 28 YAC clone29 YAC clone 29 YAC clone30 YAC clone 30

YAC No. YAC clone number YAC insert size (kb) Insert size of each YAC clone (kb)

Title Title of the data Sequence data file File name of the sequence data Data file (CSV) File name of CSV formatted data Data file (TogoDB) Name of the dataset on Simple search website (TogoDB) Image file File name of the image

Gene Gene. Gene names ccmC, ccmFn, ccmFc and ccmB were proposed by Faivre-Nitschke et al. (2001). Comment Comment Transcription Transcription nt: not tested T: transcribed N: not transcribed Editing site Editing site N: not transcribed Previous reports on editing sites Previous reports on editing sites Strand Strand S: sense A: antisense exon1 start Start position of exon1 exon1 end End position of exon1 exon2 start Start position of exon2 exon2 end End position of exon2 exon3 start Start position of exon3 exon3 end End position of exon3 exon4 start Start position of exon4 exon4 end End position of exon4 exon5 start Start position of exon5 exon5 end End position of exon5

Fragment no. Fragment number Position in mtDNA Position in the mitochondrial DNA sequence Fragment size(nt) Size of the fragment Position in ptDNA Position in the plastid DNA sequence (The position is based on Hiratsuka et al. (1989)) Genes Genes Substitution Number of substitutions in the plastid DNA sequence Deletion Number of nucleotide deletions in the plastid DNA sequence (Number of deletion sites is shown in parentheses) Insertion Number of nucleotide insertions in the plastid DNA sequence (Number of insertion sites is shown in parentheses) Homology(%) Percentage homology to the rice plastid DNA sequence

nuc. position Position of the sequence fragment in the rice mitochondrial genome length Length of the sequence fragment sense or antisense Sense or antisense strand +: sense -: antisense organism Source of the most closely related transposon/retrotransposon sequence kind of element Transposon or retrotransposon R: retrotransposon T: transposon accession GenBank Accession number of the most closely related transposon/retrotransposon sequence % Percentage homology to the most closely related transposon/retrotransposon sequence definition Characteristics of the most closely related transposon/retrotransposon sequence

Amino acids Amino acid binding to tRNA tRNA tRNA gene indicated by the cognate amino acid in one-letter code rice Rice +: tRNA present -: tRNA absent y: pseudogene a: mitochondrial tRNA b: plastid-like tRNA Miyata et al. (1998) was used as reference for rice trnP and trnR pseudogenes. Arabidopsis Arabidopsis +: tRNA present -: tRNA absent y: pseudogene a: mitochondrial tRNA b: plastid-like tRNA Reference: Unseld et al. (1997) sugarbeet Sugar beet +: tRNA present -: tRNA absent y: pseudogene a: mitochondrial tRNA b: plastid-like tRNA c: novel tRNA Reference: Kubo et al. (2000b)

plastid sequence No. Plastid sequence number Genes Genes on the plastid sequence Length Length of the plastid sequence Mutations of comparison with nuclear sequence Comparison with the most closely related nuclear sequence sub: substitutions del: deletions ins: insertions The total number of nucleotide alterations in the fragment is shown in parentheses Homology Percentage homology to the most closely related nuclear sequence Mutations of comparison with mt sequence Comparison with the most closely related mitochondrial sequence sub: substitutions del: deletions ins: insertions The total number of nucleotide alterations in the fragment is shown in parentheses Homology Percentage homology to the most closely related mitochondrial sequence

Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones') Clone id Clone ID 96 Plate Identification number of the 96 Plate used for PCR check of the clone Position Position in the 96 plate used for PCR check of the clone PCR products check (3'UTR) PCR products check (3'UTR): "blank"; result match to the prediction, "no"; no band, "m"; multiband. PCR products check (Full inserts) PCR products check (Full inserts): "blank"; result match to the prediction, "no"; no band, "m"; multiband. Accession id 1 DDBJ accession number 1 Accession id 2 DDBJ accession number 2

Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones') Clone name Clone name Dplate Destination Plate name, which used for PCR check of the clone Dplate Pos. Position on the Destination Plate used for PCR check of the clone PCR products check (Full inserts) PCR products check (Full inserts): "blank"; result match to the prediction, "no"; no band, "m"; multiband. Accession (5') DDBJ accession number (5') Accession (3') DDBJ accession number (3')

Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones') Spot No. Spot No. Clone name Clone name Putative Gene Identification Putative Gene Identification Destination Plate (96) Destination Plate number, which used for PCR check of the clone Dplate Pos. Position on the Destination Plate used for PCR check of the clone Source Plate Name Source Plate Name *No available data Clone Pos. in STAFFDWP Clone Pos. in STAFFDWP (STAFF Deep Well Plate) *No available data Accession No. (A) DDBJ accession number, which clone neme include A Accession No. (Z) DDBJ accession number, which clone neme include Z Primer No. Primer number *No available data to Full Spot No. to Full Spot number *No available data 384Plate Identification number of 384Plate used for spotting cDNA on the Glass 384Plate Pos. Position on the 384Plate

f_array_element f_array element number (spotted position on the glass: refer to the 'Array patterns and clones') Accession1 DDBJ accession number 1 Accession2 DDBJ accession number 2 Clone name Clone name DDBJ name Name in the definition of DDBJ Multi Similarity between sequences of cDNA clones and those of rice genome. (high to low ; A, B, C….) Mapping D : Sequence of the clone was directly used for mapping. G : Sequence of the representative clone in the group consisting of clones with similar sequences was used for mapping. Chr. Chromosome number Clone name (group) Representative clone name in the group Multi (group) Similarity between sequences of the representative clone and rice genome in the group. (high to low ; A, B, C….) Chr. (group) Chromosome number of the genome sequence similar to that of the representative clone in the group

g_Element No. g_Element number on the Rice8987 g_array, which indicates the spotting position on the glass f_Element No. f_Element number on the Rice8987 f_array, which indicates the spotting position on the glass 3UTR Element No. 3UTR Element number on the Rice8987 Array (3'UTR version), which indicates the spotting position on the glass Clone name Clone name Accession 01 DDBJ accession number 01 Accession 02 DDBJ accession number 02 Putative Identification Putative Gene Identification Destination Plate (96) Destination Plate number, which used for PCR check of the clone Dplate Pos. Position on the Destination Plate used for PCR check of the clone Full insert M /no check PCR products check (Full inserts) using the M13 RV primer and the M4 primer (TAKARA) : "blank"; result match to the prediction, "no"; no band, "m"; multiband. Mapped 3'UTR Primer seq (Upper) Mapped 3'UTR Primer sequence (Upper) Mapped 3'UTR Primer seq (Lower) Mapped 3'UTR Primer sequence (Lower) Unmapped 3'UTR Primer seq (Upper) Unmapped 3'UTR Primer sequence (Upper) Unmapped 3'UTR Primer seq (Lower) Unmapped 3'UTR Primer sequence (Lower)

Tissue ID ID of the 2D-PAGE image. Tissue type Type of organ column. "tissue": growing stage or kind of organ. "organelle": kind of organelle. Tissue Kind of organ or organelle. Gel image File name of gel image. Spot No gel image File name of gel image with spot No.

Spot ID ID of the spot. Spot No. Serial number of this spot on the gel. tissue ID ID of the 2D-PAGE image. pI pI (isoelectric point) of protein on this spot. MW MW (molecular weight) of protein on this spot. organism Plant material that user for protein extraction. tissue Tissue or organella for extracting tissue material. expression Expression of protein analysed by 2D ELITE (image analysis software of two-dimensional polyacrylamide gel electrophoresis, Amersham). spot gel image Extended gel image of the spot. Mass Spectrometry Accession No. Accession No. of homologous protein by Mascot Analysis. Mass Spectrometry Homologous Protein Definition of homologous protein by Mascot Analysis. Mass Spectrometry Score (%) Mascot score. Protein Sequencer Accession No. Accession No. of homologous protein by protein sequencer. (multiple entries) Protein Sequencer Homologous Protein Definition of homologous protein by Mascot Analysis. (multiple entries) cDNA Accession No. Accession No. of homologous cDNA. (multiple entries)

Spot ID ID of the spot. Amino sequence Amino acid sequence of this spot analysed by protein sequencer. Homologous Protein Accession No. Accession No. of homologous protein. Homologous Protein definition Definition of homologous protein. Homologous search identities (%) Identifies percentage of homologous search.

Spot ID ID of the spot. Accession NO Accession No. of homologous cDNA. Clone name Clone name of homologous cDNA. Score Score Coverage Coverage

PDB ID PDB ID of the protein Japanese name Japanese name of the organism species English name English name of the organism species Scientific name Scientific name of the organism species Protein name Name of the protein Gene name Gene name of the protein Source/Organism Organism species of the protein Compound Compound of the protein Classification Category of the protein EC number Enzyme Commission number of the protein Authors Authors of the reference Reference Reference has published the structure of the protein Key word Keyword of the function of the protein Cross reference Cross-reference with other databases Experimental method Experimental method for the protein structure determination Sequence characteristics Characteristics of the amino acid sequence Sequence Amino acid sequence of the protein Image Image file name of the three-dimensional structure of the protein

RefSeqID RefSeq ID domainSize Number of linked Domain Modeling Link to Domain (only in SimpleSearch pages) link to Domain Modeling of the same RefSeqID Link to Complex (only in SimpleSearch pages) link to Complex Modeling of the same RefSeqID GeneID Entrez Gene ID of the gene coding the protein Definition Protein name in RefSeq database chromosome Chromosome number of the gene Location Locus of the gene Sequence Amino acid sequence EC number Enzyme Commission numbers EzCatDB EzCatDB (A Database of Enzyme Catalytic Mechanisms) ID HPRD Human Protein Reference Database (HPRD) ID Swiss-Prot (only in SimpleSearch pages) link to UniProtKB/Swiss-Prot

RefSeqID RefSeq ID Link to Protein (only in SimpleSearch pages) link to Protein Basic Information of the same RefSeqID chromosome Chromosome number of the gene domainIdx Domain index (sequential) for a protein apoholoNum 1: Only apo form was modeled. 2:Only holo form. 3:Both apo and holo forms aafrom Starting amino acid residue number. aato Ending amino acid residue number. Domain description Function of the domain region (predicted based on the template protein information). apo Template Template protein in apo form. apo model PDB Link to the predicted structure. holo Template Template protein in holo form. holo model PDB Link to the predicted structure. Detected by Template search methods Ligand Binding Residues Ligand binding residues Interface Residues Protein-protein interaction residues Catalytic Residues Catalytic residues (only for enzymes) Ligand PDBchemical ID for the predicted ligands morphing 0: No animation data. 1: animation data presented.

RefSeqID RefSeq ID Link to Protein (only in SimpleSearch pages) link to Protein Basic Information of the same RefSeqID regionFrom Starting amino acid residue number. regionTo Ending amino acid residue number. model PDB (only in SimpleSearch pages) link to model structure (PDB) Oligomer homo oligomer / hetero oligomer Model Model index (sequential) for a protein Template Template for the complex modeling Partner ID RefSeq ID of the counterpart protein in the complex.

RefSeqID RefSeq ID Domain_type Type of domain structure (apo or holo) Template Template protein name Query_from Starting amino acid residue number of the aligned region of the target protein. Query_to Ending amino acid residue number of the aligned region of the target protein. Query_alignment Alignment sequence (query) Template_from Starting amino acid residue number of the aligned region of the template protein. Template_to Ending amino acid residue number of the aligned region of the template protein. Template_alignment Alignment sequence (template) Alignment_line Line of alignment Identity(%) Sequence identity

seqname Sequence name source Analysis software feature Feature of the sequence region start Start sequence number of the region end End sequence number of the region score Confidence score of the region strand Strand of the region frame Codon frame of the region attributes Other attributes

ASG1 Anterior silk gland (biological replicate 1) ASG2 Anterior silk gland (biological replicate 2) ASG3 Anterior silk gland (biological replicate 3) MSG_A1 Anterior part of the middle silk gland (biological replicate 1) MSG_A2 Anterior part of the middle silk gland (biological replicate 2) MSG_A3 Anterior part of the middle silk gland (biological replicate 3) MSG_M1 Middle part of the middle silk gland (biological replicate 1) MSG_M2 Middle part of the middle silk gland (biological replicate 2) MSG_M3 Middle part of the middle silk gland (biological replicate 3) MSG_P1 Posterior part of the middle silk gland (biological replicate 1) MSG_P2 Posterior part of the middle silk gland (biological replicate 2) MSG_P3 Posterior part of the middle silk gland (biological replicate 3) PSG1 Posterior silk gland (biological replicate 1) PSG2 Posterior silk gland (biological replicate 2) PSG3 Posterior silk gland (biological replicate 3) MG1 Midgut (biological replicate 1) MG2 Midgut (biological replicate 2) MG3 Midgut (biological replicate 3) FB1 Fat body (biological replicate 1) FB2 Fat body (biological replicate 2) FB3 Fat body (biological replicate 3) MT1 Malpighian tubules (biological replicate 1) MT2 Malpighian tubules (biological replicate 2) MT3 Malpighian tubules (biological replicate 3) TT1 Testis (biological replicate 1) TT2 Testis (biological replicate 2) TT3 Testis (biological replicate 3) OV1 Ovary (biological replicate 1) OV2 Ovary (biological replicate 2) OV3 Ovary (biological replicate 3) BN_FB1 Fat body from SRA (biological replicate 1) BN_FB2 Fat body from SRA (biological replicate 2) BN_FB3 Fat body from SRA (biological replicate 3) BN_MG1 Midgut from SRA (biological replicate 1) BN_MG2 Midgut from SRA (biological replicate 2) BN_MG3 Midgut from SRA (biological replicate 3) BN_MT1 Malpighian tubules from SRA (biological replicate 1) BN_MT2 Malpighian tubules from SRA (biological replicate 2) BN_MT3 Malpighian tubules from SRA (biological replicate 3) BN_SG1 Silk gland from SRA (biological replicate 1) BN_SG2 Silk gland from SRA (biological replicate 2) BN_SG3 Silk gland from SRA (biological replicate 3) BN_TT1 Testis from SRA (biological replicate 1) BN_TT2 Testis from SRA (biological replicate 2) BN_TT3 Testis from SRA (biological replicate 3) target_id Unique ID allocated to each transcript in reference transcriptomic data

human_gname Symbol of top hit human gene. fly_gname Symbol of top hit Drosophila gene. target_id Unique ID allocated to each transcript in reference transcriptomic data

SKIP ID SKIP ID Organism(En) Organism of this cell (English) Organism(Ja) Organism of this cell (Japanese) Cell Type(En) Cell Type (English) Cell Type(Ja) Cell Type (Japanese) Cell Tissue(En) Cell Tissue (English) Cell Tissue(Ja) Cell Tissue (Japanese) Cell Origin Status of cell origin Cell Name 1(En) Cell Name 1 (English) Cell Name 1(Ja) Cell Name 1 (Japanese) Cell Name 2(En) Cell Name 2 (English) Cell Name 2(Ja) Cell Name 2 (Japanese) Disease Name 1(Ja) Disease Name 1 (Japanese) ICD Code 1 ICD Code 1 Disease Name 1(En) Disease Name 1 (English) OMIM1 OMIM ID 1 Disease Name 2(Ja) Disease Name 2 (Japanese) ICD Code 2 ICD Code 2 Disease Name 2(En) Disease Name 2 (English) OMIM 2 OMIM ID 2 Disease Name 3(Ja) Disease Name 3 (Japanese) ICD Code 3 ICD Code 3 Disease Name 3(En) Disease Name 3 (English) OMIM 3 OMIM ID 3 Age Age of donor Age Range Age range of donor Sex Sex of donor Race(En) Race of donor (English) Race(Ja) Race of donor (Japanese) Genetic Diagnosis Genetic Diagnosis or none Not Detected Not Detected or detected in genetic diagnosis Description(En) Description of this cell (English) Description(Ja) Description of this cell (Japanese) Cell Morphology Cell Morphology Grade Cell provided by (research or clinic) Vector Vector to cultivate this cell Transgene Transgene to this cell Adhesiveness Cell adhesiveness Feeder Feeder cell is used or not Feeder Cell Feeder cell name Medium Medium to cultivate this cell Genome Editing Genome Editing method in the cultivation CO2 CO2 concentration in the cultivation Mycoplasma Detection of Contaminants Mycoplasma or none Detection of Contaminants Mycoplasma Method of Detection of Contaminants Mycoplasma Pluripotent Markers Pluripotent Markers Assay or none Pluripotent Markers Assay Method of Pluripotent Markers Assay in vitro Differentiation in vitro Differentiation Assay or none in vitro Differentiation Assay Method of in vitro Differentiation Assay in vivo Differentiation in vivo Differentiation Assay or none in vivo Differentiation Assay Method of in vivo Differentiation Assay Other 1 Assay Other 1 Assay or none Other 1 Assay Method Method of Other 1 Assay Other 2 Assay Other 2 Assay or none Other 2 Assay Method Method of Other 2 Assay Other 3 Assay Other 3 Assay or none Other 3 Assay Method Method of Other 3 Assay Karyotype Karyotype Assay or none Karyotype Assay Method of Karyotype Assay Remaining Vector Detection Remaining Vector Detection Assay or none Remaining Vector Detection Assay Method of Remaining Vector Detection Assay STR STR analysis or none HLA HLA typing or none Stem Cell Transcriptome analysis Stem Cell Transcriptome analysis or none Stem Cell Transcriptome analysis Assay Stem Cell Transcriptome analysis Assay or none Author Name(En) Author Name (English) Author Name(Ja) Author Name (Japanese) Author Organization(En) Author Organization (English) Author Organization(Ja) Author Organization (Japanese) Author Contact Email Author Contact Email PI Organization(En) Principal Investigator (PI) Organization (English) PI Organization(Ja) PI Organization (Japanese) PI Name(En) PI Name (English) PI Name(Ja) PI Name (Japanese) PI Contact Email PI Contact Email Availability Stemcell Availability Provider Organization(En) Provider Organization (English) Provider Organization(Ja) Provider Organization (Japanese) Provider Email Provider Email Provider URL Provider URL Ethical Statement(En) Ethical Statement (English) Ethical Statement(Ja) Ethical Statement (Japanese) Terms of Use(En) Terms of Use (English) Terms of Use(Ja) Terms of Use (Japanese) PubMed ID PubMed ID of article (reference) DOI DOI (Digital Object Identifier) of article Title Article Title Authors Article Authors Journal Journal which contains the article Year Publishing Year of the journal Volume Volume of the journal Issue Issue of the journal Pages Pages in the journal URL Article URL Free input Others about the article Note Comment

URL Website URL for the society Name Society name Abbreviation Abbreviation for the society name Class Classification for the society Membership fee Membership fee Academy remarks Academy remarks Contact: E-Mail Contact address Free public site: Free public site URL Free public site URL Paid public site: Paid public site URL Paid public site URL Academic journal: Name Name for the academic journal published by the society Academic journal: Language of text Language of text for the journal Academic journal: Language of abstract Language of abstract for the journal Academic journal: URL URL for the journal Academic journal: Print ISSN Print ISSN for the journal Academic journal: Online ISSN Online ISSN for the journal Academic journal: Online ISSN:URL of published range URL of published range for the journal Academic journal: Term of issuance Term of issuance for the journal

Accession Identified protein accession number Gel ID Gel ID where the protein is separated Spot ID Spot ID on thegel Description Description of the protein Exp pI Measured isoelectric point of the protein Exp Mw Measured molecular weight of the protein

Gel ID Gel ID Condition Experiment sample condition pI Range of measured isoelectric point in the gel Mw Range of measured molecular weight in the gel Identified spots Number of identified spots in the gel Identified proteins Number of identified proteins in the gel Gel image Gel image (only in simple search)

Gel ID Gel ID Spot ID Spot ID X X coordinate on the gel Y Y coordinate on the gel pI Protein isoelectric point on the spot Mw Protein molocular weight on the spot

Accession (Soybean) Protein accession number in soybean Accession (Arabidopsis) Protein accession number in arabidopsis Description Description of the protein Stage Soybean development stage ("Seed" or days after sowing) Organ Organ of soybean Organelle Organelle of soybean Stress Condition of flood stress Mass Protein molecular weight measured by mass spectrometer Protein content (mol %) Protein molar concentration in the sample emPAI Protein emPAI concentration in the sample Peptides Number of peptides in the sample which match the protein Score Matching score about the above

Primer HiCEP primer set (5' end - 3' end) Peak No Peak number of DNA sequences identified by sequencer 2(0) Height min Sample: 2 days after seeding, 0 days after flooding Minimum peak value in sequencing 2(0) Height max Sample: 2 days after seeding, 0 days after flooding Maximum peak value in sequencing 2.5(0) Height min Sample: 2.5 days after seeding, 0 days after flooding (control) Minimum peak value in sequencing 2.5(0) Height max Sample: 2.5 days after seeding, 0 days after flooding (control) Maximum peak value in sequencing 2.5(0.5) Height min Sample: 2.5 days after seeding, 0.5 days after flooding Minimum peak value in sequencing 2.5(0.5) Height max Sample: 2.5 days after seeding, 0.5 days after flooding Maximum peak value in sequencing 3(0) Height min Sample: 3 days after seeding, 0 days after flooding (control) Minimum peak value in sequencing 3(0) Height max Sample: 3 days after seeding, 0 days after flooding (control) Maximum peak value in sequencing 3(1) Height min Sample: 3 days after seeding, 1 days after flooding Minimum peak value in sequencing 3(1) Height max Sample: 3 days after seeding, 1 days after flooding Maximum peak value in sequencing 3.5(0) Height min Sample: 3.5 days after seeding, 0 days after flooding (control) Minimum peak value in sequencing 3.5(0) Height max Sample: 3.5 days after seeding, 0 days after flooding (control) Maximum peak value in sequencing 3.5(1.5) Height min Sample: 3.5 days after seeding, 1.5 days after flooding Minimum peak value in sequencing 3.5(1.5) Height max Sample: 3.5 days after seeding, 1.5 days after flooding Maximum peak value in sequencing 4(0) Height min Sample: 4 days after seeding, 0 days after flooding (control) Minimum peak value in sequencing 4(0) Height max Sample: 4 days after seeding, 0 days after flooding (control) Maximum peak value in sequencing 4(2) Height min Sample: 4 days after seeding, 2 days after flooding Minimum peak value in sequencing 4(2) Height max Sample: 4 days after seeding, 2 days after flooding Maximum peak value in sequencing Size min Minimum molecular weight of DNA in seuquencing Size max Maximum molecular weight of DNA in seuquencing 1_Cluster_No Cluseter number of 1st clustering (0-31) 2_Cluster_No Cluseter number of 2nd clustering (1-65) Target records are filtered in the following conditions: ・Classified in "31" of 1st clutering ・max peak / min peak > 3 3_Peak_No Graph number in "Soybean omics data" Target records are filtered in the following conditions: ・peak value in treated / peak value in control > 20

Organ Organ of soybean Stress Stress on soybean Spot No Spot No on gels Homologous protein Homologous protein of measured one Accession No Accession No of homologous protein Mr(kDa)-theory Theoretical molecular weight of homologous protein Mr(kDa)-exp Measured molecular weight pI-theory Protein isoelectric point of homologous protein pI-exp Measured protein isoelectric point F.C. Fold change compared with no treatment (without stress) soybean samples

Organism Name of a targeted organism. Datatype Describes specific type of data that was represented in the BDML file Basedon Speficifies whether the data was gathered from an in vivo measurement or from a computer simulation. Contributor Names of contributors who produced/collected the data. Number of BDML-files Number of BDML-files Contact Information Contact information for the BDML file. Summary of methods Methods/procedures used to obtain the data described in the BDML file. PubMed ID PubMed ID of the original published paper. License License information of the BDML file. Data Scale (XYZ,T) Scale and unit of coordinates and time. Dataset Description Description about the dataset.

Title Title of the BDML file. Description Detailed information about the data described in the BDML file Organism Name of a targeted organism. Datatype Describes specific type of data that was represented in the BDML file Local ID Internal or local identifier used to identify the BDML file. Basedon Speficifies whether the data was gathered from an in vivo measurement or from a computer simulation. Contributor Names of contributors who produced/collected the data. Contact Information Contact information for the BDML file. Summary of methods Methods/procedures used to obtain the data described in the BDML file. PubMed ID PubMed ID of the original published paper. License License information of the BDML file. Schema Version of BDML schema. BDML ID Unique ID of the BDML file. Data Scale (XYZ,T) Scale and unit of coordinates and time. Source A URL link to original sources such as microscope images for an experimental measurement or files of mathematical model for a computer simulation. BDML file A URL link to download a BDML file PDPML file A URL link to download a PDPML file SSBD web page A URL link to view a summay page SSBD-OMERO web page A URL link to view a set of microscopy images

Name English common name of species Scientific Name Scientific name of species Taxonomy ID NCBI Taxonomy ID (Link to NCBI in Simple Search) Icon Taxonomy Taxonomy information which were used to refine icons in original database interface. Icon (Large) File name of the large-sized icon (The icon is displayed in Simple Search.) Icon (Large) No Background File name of the large-sized icon with no background (The icon is displayed in Simple Search.) Icon (Small) File name of the small-sized icon (The icon is displayed in Simple Search.) Icon (Small) No Background File name of the small-sized icon with no background (The icon is displayed in Simple Search.) URL of Icon (Large) URL to diplay the large-sized icon URL of Icon (Large) No Background URL to diplay the large-sized icon with no background URL of Icon (Small) URL to diplay the small-sized icon URL of Icon (Small) No Background URL to diplay the small-sized icon with no background Comment Link to Simple Search for comment

Species Name English common name of species Scientific Name Scientific name of species Icon File name of the icon (The icon is displayed in Simple Search.) Image File name of the image posted on the icon entry (The image is displayed in Simple Search.) License License of the image posted on the icon entry (This License information is shown at "Image" column in Simple Search.) Comment Comment posted on the icon entry Name Name who posted the commnet Created Date Date when the comment was posted Last Modified Date Last modified date of the comment

ID ID of the test Type Type of the measuring instrument Species Species (Oryza sativa) Material Strain Light condition Light condition Temperature Temperature Humidity Humidity Medium Medium Growth Chamber Growth Chamber Soil Soil Imaging system Imaging system Camera Camera Induction of germination / Period Period of imaging (for ID=1) or start time of germination induction and imaging (for other entries) Duration of observation Duration of observation Intervals of imaging Intervals of imaging Growth data Graph of chronological changes in growth Image list Name list of images Large image The zip file of the images (Large image) Small image The zip file of the images (Small image) First image First image (only Simple search site) Last image Last image (only Simple search site)

Sequence Collection ID Sequential serial number assigned to each genome. Classification Biological classification (Archaea, Bacteria and Eukaryota) Organism Name Name of the organism. Chromosome number is added to the name if the organism has multiple chromosomes. Locus RefSeq ID of the genome sequence. FASTA File Name of the FASTA file where the genome sequence is listed.

Sequence ID Sequential serial number assigned to each amino acid sequence. Sequence Collection ID Sequential serial number assigned to each genome. New Approach Result of predicting transmembrane helical protein using a newly developed method which is performed by the following steps. Identify the β-barrel membrane proteins using the dipeptide compositions of β-barrel membrane proteins and globular proteins. Refine the search using the dipeptide compositions of β-barrel membrane proteins and transmembrane helical proteins. Remove the shorter sequences (proteins with less than 50 amino acid residues). Eliminate transmembrane helical proteins using SOSUI, a prediction system for transmembrane helical proteins, using the criterion that it identified at least two membrane spanning helical segments. Exclude globular and transmembrane helical proteins which have &gt; 70% sequence identity and 80% coverage with that deposited in PDB. Exclude globular and transmembrane helical proteins which have &gt; 80% sequence identity with that deposited in SWISS-PROT database. SOSUI Result of predicting transmembrane helical protein using SOSUI. Amino Acid Result of predicting β-barrel membrane protein with a statistical method using amino acid composition. (TMBETADISC-COMP) Dipeptide Result of predicting β-barrel membrane protein with a statistical method using residue pair preference. (TMBETADISC_DIPEPTIDE) Motif Result of predicting β-barrel membrane protein with a statistical method using motifs. (TMBETADISC-MOTIF) SVM Result of predicting β-barrel membrane protein with a machine learning method using amino acid composition and residue pair preference. (TMBETA-SVM) Header Header line of the amino acid sequence entry in the FASTA file. Sequence Amino acid sequence

Entry Entry Residue(mutation) Name of residue with mutation Residue Name of residue Functionally important Functionally important or not Function of the protein Function of the protein Location Location of residue in the protein Protein Name(abbreviation) Protein Name(abbreviation) Source(scientific name) Source of protein (scientific name) Source(english name) Source(english name) Authors Authors of reference Journal Reference Journal Reference PMID PubMed ID of reference Experiments Experiments Experimental data The value with "Parameter" shows a measurement value in experiments. Parameter Experimental parameter Methods/conditions Experimental methods/conditions PDB ID PDB ID of the protein structure ASA Accessible surface area Sec. Str Secondary structure of this protein - G: 3-10 helix - H: Helix - L: Loop Uniprot ID UniProt ID of protein Type Type of protein Remarks Remarks Keywords Keywords

Picture ID Picture ID Thumbnail Thumbnail Title (jp) Title (Japanese) Title (en) Title (English) Scientific Name Scientific Name Taxonomy ID Taxonomy ID Tags Tags associated with the image

Project ID Project ID Project Theme Theme of the project Project Theme (short) Theme of the project (short ver.) Principal Investigator Principal Investigator of the project Affiliation Affiliation of the project Backgrounds Backgrounds of the project Highlights Highlights of the project Outline Outline of the project Review Reviews or original papers on the project (In the cases of multiple items, they are arranged in the same order as PubMed ID.) PubMed ID PubMed ID (In the cases of multiple items, they are arranged in the same order as Review.) CSML File Name of the Network data (CSML file) (Linked to the Network data in the Simple Search site.)

Project ID Project ID Sub Group Sub group of the protein Symbol Symbol of the protein Synonym Synonym of the protein Wiki Search term in wikipedia Full Name Full name of the protein Other Names Other names of the protein TaxId Taxon identifer in UniProt Taxonomy Organism Organism of the protein Entrez Gene ID in NCBI Gene UniProt UniProt KB accession number GNP Gene ID in GNP (Genome Network Platform) (NCBI Gene ID) Struct. PDB PDB ID in PDBj (Protein Data Bank Japan) Struct. P3K PDB ID in Protein 3000 Structure Gallery Struct. TPRP PDB ID in TP Structure Gallery PPI GNP Gene ID in PPI in GNP (NCBI Gene ID) PCI PDB ID in PCI TP Article PMID (PubMed ID) in PubMed Press Release TP press release ID

Data type Types of acquired data. Classified into nine types including "Prokaryotic complete genome", "Prokaryotic draft genome (WGS)", "Plant", "Fungus", "Virus", "Phage", "Chloroplast", "Environmental sample (ENV) from GenBank" and "Environmental sample (ENV) from Sequence Read Archive". Sequence ID Sequence ID Genome ID Genome ID (Genome ID of DDBJ GIB is used.) Phylum/Class Taxon name Species Species name Start position tRNA gene start position on the genome End position tRNA gene end position on the genome Direction Direction of tRNA gene on the genome Amino Acid Amino acid type Anticodon Anticodon 1st Intron start position Start position of first intron 1st Intron end position End position of first intron Seq tRNA sequence Upstream seq. tRNA gene upstream sequence (10 bps) tRNA1-7 1st to 7th nucleotides in the clover-leaf secondary structures (*1) of tRNA gene tRNA8-9 8th to 9th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA10-13 10th to 13th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA14-21 14th to 21st nucleotides in the clover-leaf secondary structures of tRNA gene tRNA22-25 22nd to 25th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA26 26th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA27-31 27th to 31st nucleotides in the clover-leaf secondary structures of tRNA gene tRNA32-38 32nd to 38th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA39-43 39th to 43rd nucleotides in the clover-leaf secondary structures of tRNA gene tRNA44-48 44th to 48th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA49-53 49th to 53rd nucleotides in the clover-leaf secondary structures of tRNA gene tRNA54-60 54th to 60th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA61-65 61st to 65th nucleotides in the clover-leaf secondary structures of tRNA gene tRNA66-72 66th to 72nd nucleotides in the clover-leaf secondary structures of tRNA gene tRNA73-76 73rd to 76th nucleotides in the clover-leaf secondary structures of tRNA gene Downstream seq. tRNA gene downstream sequence (10 bps) 1st Intron seq. First intron sequence 2nd Intron start position Start position of second intron 2nd Intron end position End position of second intron 2st Intron seq. Second intron sequence Decision from Dr. Muto Determination 1 (Dr. Muto) Decision from Dr. Inokuchi Determination 2 (Dr. Inokuchi) Decision from Dr. Yamada Determination 3 (Dr. Yamada) Comment of Dr. Muto Comment 1 (Dr. Muto) Comment of Dr. Inokuchi Comment 2 (Dr. Inokuchi) Comment of Dr. Yamada Comment 3 (Dr. Yamada) Final decision Final Determination Comments Comment Original database Genome sequence source information

symbol Symbol of the protein name Name of the protein organism Organism of the protein mRNA sequence GI number of the mRNA sequence (Link to the NCBI Nucleotide in the Simple search site) protein sequence GI number of the Amino Acid sequence (Link to the NCBI Protein in the Simple search site) entrez Gene ID (NCBI Gene) uniprot UniProt Accession number wikipedia Search term in Wikipedia ec Enzyme Commission number omim OMIM ID (Online Mendelian inheritance in Man) map Location of the gene on a chromosome or its chromosome number pdb PDB ID (PDBj: Protein Data Bank Japan) kegg pathway ID of the KEGG pathway candidate inhibitor Name of candidate inhibitor of the protein drugport id DrugBank ID of candidate inhibitor

Bait ORF The ORF name of Bait, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/). Bait gene name The gene name of Bait, and the standard name in the SGD. Bait description The annotation of Bait, and description in the SGD. Rows with this bait as bait The number of rows (interactions) having this Bait ORF as the Bait ORF, and the link to the search results (for TogoDB only). Rows with this bait as prey The number of rows (interactions) having this Bait ORF as the Prey ORF, and the link to the search results (for TogoDB only). Prey ORF The ORF name of Prey, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org). Prey gene name The gene name of Prey, and the standard name in the SGD. Prey description The annotation of Prey, and description in the SGD. Rows with this prey as prey The number of rows (interactions) having this Prey ORF as the Prey ORF, and the link to the search results (for TogoDB only). Rows with this prey as bait The number of rows (interactions) having this Prey ORF as the Bait ORF, and the link to the search results (for TogoDB only). Literature on bait(YPD) The number of articles concerning Bait, obtained from YPD (Yeast Proteome Database)(*1). Literature on prey(YPD) The number of articles concerning Prey, obtained from YPD. Literature shared by bait and prey The number of articles common to Bait and Prey, as calculated on the basis of the number of articles obtained from the YPD. Literature sharing score The score concerning co-occurrence of Prey and Bait in the literature, calculated by the calculation formula. Calculation formula for the score: https://dbarchive.biosciencedbc.jp/images/db_meta/yeast_y2h/literature_sharing_score.png CuraGen(0 or 1) Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*2) S. Fields(0 or 1) Investigation by S. Fields (0 or 1), obtained from Uetz et al. Association(0 or 1,YPD) Association (0 or 1), obtained from the YPD. Complex (0 or 1,YPD) Formation of complex (0 or 1), obtained from the YPD. Synthetic lethality(0 or 1,YPD) Synthetic lethality (0 or 1), obtained from the YPD. Co-induced by(YPD) Factor that induces expression of both genes, obtained from the YPD. Co-repressed by(YPD) Factor that suppresses expression of both genes, obtained from the YPD. Not affected by(YPD) Factor that does not affect expression of these genes, obtained from the YPD. Interologs The number of interactions that exist between the interacting protein and the ortholog of other species, obtained from the Database of Interacting Proteins(*3). Expression similarity (BRITE) Expression data obtained from KEGG BRITE(*4). (High values only, 0.9 or greater) Alternative path with 1 intervening protein The number of paths other than this interaction mediated by one intermediate protein, calculated from the full data. Alternative path with 2 intervening proteins The number of paths other than this interaction mediated by two intermediate proteins, calculated from the full data. IST hit Number of hits of Interaction Sequence Tags (IST) (The number of detected interactions and the indicator of reproducibility) IST hit in the opposite bait/prey orientation The IST hit number for a combination in which Bait and Prey are in the reverse direction.

Bait ORF The ORF name of Bait, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/). Bait gene name The gene name of Bait, and the standard name in the SGD. Bait description The annotation of Bait, and description in the SGD. Rows with this bait as bait The number of rows (interactions) having this Bait ORF as the Bait ORF, and the link to the search results (for TogoDB only). Rows with this bait as prey The number of rows (interactions) having this Bait ORF as the Prey ORF, and the link to the search results (for TogoDB only). Prey ORF The ORF name of Prey, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org). Prey gene name The gene name of Prey, and the standard name in the SGD. Prey description The annotation of Prey, and description in the SGD. Rows with this prey as prey The number of rows (interactions) having this Prey ORF as the Prey ORF, and the link to the search results (for TogoDB only). Rows with this prey as bait The number of rows (interactions) having this Prey ORF as the Bait ORF, and the link to the search results (for TogoDB only). Literature on bait(YPD) The number of articles concerning Bait, obtained from YPD (Yeast Proteome Database)(*1). Literature on prey(YPD) The number of articles concerning Prey, obtained from YPD. Literature shared by bait and prey The number of articles common to Bait and Prey, as calculated on the basis of the number of articles obtained from the YPD. Literature sharing score The score concerning co-occurrence of Prey and Bait in the literature, calculated by the calculation formula. Calculation formula for the score: https://dbarchive.biosciencedbc.jp/images/db_meta/yeast_y2h/literature_sharing_score.png CuraGen(0 or 1) Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*2) S. Fields(0 or 1) Investigation by S. Fields (0 or 1), obtained from Uetz et al. Association(0 or 1,YPD) Association (0 or 1), obtained from the YPD. Complex (0 or 1,YPD) Formation of complex (0 or 1), obtained from the YPD. Synthetic lethality(0 or 1,YPD) Synthetic lethality (0 or 1), obtained from the YPD. Co-induced by(YPD) Factor that induces expression of both genes, obtained from the YPD. Co-repressed by(YPD) Factor that suppresses expression of both genes, obtained from the YPD. Not affected by(YPD) Factor that does not affect expression of these genes, obtained from the YPD. Interologs The number of interactions that exist between the interacting protein and the ortholog of other species, obtained from the Database of Interacting Proteins(*3). Expression similarity (BRITE) Expression data obtained from KEGG BRITE(*4). (High values only, 0.9 or greater) Alternative path with 1 intervening protein The number of paths other than this interaction mediated by one intermediate protein, calculated from the full data. Alternative path with 2 intervening proteins The number of paths other than this interaction mediated by two intermediate proteins, calculated from the full data. IST hit Number of hits of Interaction Sequence Tags (IST) (The number of detected interactions and the indicator of reproducibility) IST hit in the opposite bait/prey orientation The IST hit number for a combination in which Bait and Prey are in the reverse direction.

Bait ORF The ORF name of Bait, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/). Bait gene name The gene name of Bait, and the standard name in the SGD. Bait description The annotation of Bait, and description in the SGD. Rows with this bait as bait The number of rows (interactions) having this Bait ORF as the Bait ORF, and the link to the search results (for TogoDB only). Rows with this bait as prey The number of rows (interactions) having this Bait ORF as the Prey ORF, and the link to the search results (for TogoDB only). Prey ORF The ORF name of Prey, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org). Prey gene name The gene name of Prey, and the standard name in the SGD. Prey description The annotation of Prey, and description in the SGD. Rows with this prey as prey The number of rows (interactions) having this Prey ORF as the Prey ORF, and the link to the search results (for TogoDB only). Rows with this prey as bait The number of rows (interactions) having this Prey ORF as the Bait ORF, and the link to the search results (for TogoDB only). Literature on bait(YPD) The number of articles concerning Bait, obtained from YPD (Yeast Proteome Database)(*2). Literature on prey(YPD) The number of articles concerning Prey, obtained from YPD. Literature shared by bait and prey The number of articles common to Bait and Prey, as calculated on the basis of the number of articles obtained from the YPD. Literature sharing score The score concerning co-occurrence of Prey and Bait in the literature, calculated by the calculation formula. Calculation formula for the score: https://dbarchive.biosciencedbc.jp/images/db_meta/yeast_y2h/literature_sharing_score.png CuraGen(0 or 1) Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*3) S. Fields(0 or 1) Investigation by S. Fields (0 or 1), obtained from Uetz et al. Association(0 or 1,YPD) Association (0 or 1), obtained from the YPD. Complex (0 or 1,YPD) Formation of complex (0 or 1), obtained from the YPD. Synthetic lethality(0 or 1,YPD) Synthetic lethality (0 or 1), obtained from the YPD. Co-induced by(YPD) Factor that induces expression of both genes, obtained from the YPD. Co-repressed by(YPD) Factor that suppresses expression of both genes, obtained from the YPD. Not affected by(YPD) Factor that does not affect expression of these genes, obtained from the YPD. Interologs The number of interactions that exist between the interacting protein and the ortholog of other species, obtained from the Database of Interacting Proteins(*4). Expression similarity (BRITE) Expression data obtained from KEGG BRITE(*5). (High values only, 0.9 or greater) Alternative path with 1 intervening protein The number of paths other than this interaction mediated by one intermediate protein, calculated from the full data. Alternative path with 2 intervening proteins The number of paths other than this interaction mediated by two intermediate proteins, calculated from the full data. IST hit Number of hits of Interaction Sequence Tags (IST) (The number of detected interactions and the indicator of reproducibility) IST hit in the opposite bait/prey orientation The IST hit number for a combination in which Bait and Prey are in the reverse direction.

Bait ORF The ORF name of Bait, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/). Bait gene name The gene name of Bait, and the standard name in the SGD. Bait description The annotation of Bait, and description in the SGD. Rows with this bait as bait The number of rows (interactions) having this Bait ORF as the Bait ORF, and the link to the search results (for TogoDB only). Rows with this bait as prey The number of rows (interactions) having this Bait ORF as the Prey ORF, and the link to the search results (for TogoDB only). Prey ORF The ORF name of Prey, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org). Prey gene name The gene name of Prey, and the standard name in the SGD. Prey description The annotation of Prey, and description in the SGD. Rows with this prey as prey The number of rows (interactions) having this Prey ORF as the Prey ORF, and the link to the search results (for TogoDB only). Rows with this prey as bait The number of rows (interactions) having this Prey ORF as the Bait ORF, and the link to the search results (for TogoDB only). Literature on bait(YPD) The number of articles concerning Bait, obtained from YPD (Yeast Proteome Database)(*2). Literature on prey(YPD) The number of articles concerning Prey, obtained from YPD. Literature shared by bait and prey The number of articles common to Bait and Prey, as calculated on the basis of the number of articles obtained from the YPD. Literature sharing score The score concerning co-occurrence of Prey and Bait in the literature, calculated by the calculation formula. Calculation formula for the score: https://dbarchive.biosciencedbc.jp/images/db_meta/yeast_y2h/literature_sharing_score.png CuraGen(0 or 1) Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*3) S. Fields(0 or 1) Investigation by S. Fields (0 or 1), obtained from Uetz et al. Association(0 or 1,YPD) Association (0 or 1), obtained from the YPD. Complex (0 or 1,YPD) Formation of complex (0 or 1), obtained from the YPD. Synthetic lethality(0 or 1,YPD) Synthetic lethality (0 or 1), obtained from the YPD. Co-induced by(YPD) Factor that induces expression of both genes, obtained from the YPD. Co-repressed by(YPD) Factor that suppresses expression of both genes, obtained from the YPD. Not affected by(YPD) Factor that does not affect expression of these genes, obtained from the YPD. Interologs The number of interactions that exist between the interacting protein and the ortholog of other species, obtained from the Database of Interacting Proteins(*4). Expression similarity (BRITE) Expression data obtained from KEGG BRITE(*5). (High values only, 0.9 or greater) Alternative path with 1 intervening protein The number of paths other than this interaction mediated by one intermediate protein, calculated from the full data. Alternative path with 2 intervening proteins The number of paths other than this interaction mediated by two intermediate proteins, calculated from the full data. IST hit Number of hits of Interaction Sequence Tags (IST) (The number of detected interactions and the indicator of reproducibility) IST hit in the opposite bait/prey orientation The IST hit number for a combination in which Bait and Prey are in the reverse direction.