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Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License
Silkworm, Bombyx mori, reference transcriptome data 10.18908/lsdba.nbdc02443-000
Microarray Data and other Gene Expression Databases
Annotation
Bombyx mori (7091)

The data collection contain Bombyx mori reference transcriptomic data and related data. The reference transcriptomic data was constructed from new reference genome data (Kawamoto et al., 2019, Insect biochemistry and molecular biology ) and RNAseq data of multiple tissues in Bombyx mori P50T strain.
"Metadata of reference transcriptomic data" is gtf file showing position of each transcript in the new reference genome.
"Expression data of each transcript in multiple tissue" is matrix gene expression files showing tpm values of each transcript in multiple tissues.
"Annotations of each transcript" is annotation file showing Blast results of each transcript against human and Drosophila protein data set.
"Predicted amino acid sequences in the reference transcriptomic data" is a multi fasta file of amino acid sequence predicted with from the reference transcriptomic data.

CC BY-SA
GGGenome dataset 10.18908/lsdba.nbdc01424-000
Nucleotide Sequence Databases

GGGenome is a tool for fast and sensitive search for genomic and transcript sequence. You can use it in Web (https://GGGenome.dbcls.jp/) and as a distributed Docker container. If you use the Docker container, you have to set this dataset in it. Contact the above "Contact address" about the distribution of GGGenome container.
About the reference sequence data (fasta format) in this dataset, you can use it for another purpose.

GGGenome exhaustively searches short sequences allowing mismatches and gaps.

Database Center for Life Science

CC BY
MeCab user dictionary for science technology term 10.18908/lsdba.nbdc02358-000.V002
dictionary

We have made a user dictionary of morphological analysis engine MeCab (http://taku910.github.io/mecab/) headwords and synonyms of JST Thesaurus (2015 edition) . The dictionary items are based on IPA dictionary and encoded in UTF-8. Entries with zenkaku alphabets, numerals and symbols converted into corresponding hankaku characters are also included.
Please note that this dictionary can not be used as a thesaurus because information on relations between words is not included in the dictionary.

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CC BY
AOE
(All Of gene Expression)
10.18908/lsdba.nbdc00467-000
Microarray Data and other Gene Expression Databases

An index of public gene expression database.

Direct data access from the histogram, and make the table with selecte entries.
Updated data ranking by organisms and by methods enhances searchability of archived data.
Dynamic histogram for selected organisms and methods can be produced only by click operation.

CC BY
FANTOM5
(Functional Annotation of the Mammalian Genome)
10.18908/lsdba.nbdc01389-000.V003
Homo sapiens (9606)
Mus musculus (10090)
Rattus norvegicus (10116)
Canis lupus familiaris (9615)
Macaca mulatta (9544)
Gallus gallus (9031)

FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM has since developed and expanded over time to encompass the fields of transcriptome analysis. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the 'elements' - the transcripts - to an understanding of the 'system' - the transcriptional regulatory network, in other words the 'system' of an individual life form. In FANTOM5, we have systematically investigated exactly what are the sets of genes used in virtually all cell types across the human body, and the genomic regions which determine where the genes are read from. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human. The resource provides raw and processed data obtained in the FANTOM5 project.

The FANTOM5 resources provides a comprehensive map of gene activity across the human body, and provides a holistic view of the complex networks that regulate gene expression across the wide variety of cell types that make up a human being. The resource can be a foundamental tool to define normal cells in human bodies. These findings will help in the identification of genes involved in disease and the development of personalized and regenerative medicine.

CC BY
Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License