FANTOM5

2019/03/29

Web Site: http://fantom.gsc.riken.jp/5/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/fantom5/

The database on activities of transcripts and transcription factors in various cell species of human and mouse.

README Content

1. Database Component
2. Data Description
3. License
4. Update History
5. Literature
6. Contact address

1. Database Component

1. README
2. HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
3. CAGE peaks
4. Pathway enrichment and co-expression cluster analysis
5. Enhancers
6. Results of de-novo and Motif activity analyses
7. CAGE_peaks_annotation
8. Sample ontology, GOstat and ontology term enrichment
9. CAGE peaks identified as true TSS by TSS classifier
10. (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
11. (reprocessed)CAGE peaks
12. (reprocessed)CAGE_peaks_annotation
13. (reprocessed)CAGE_peaks_expression
14. (reprocessed)pooled_ctss
15. DRA_accession_tables
16. Gene_level_expression
17. Summary_CAGEScan
18. (reprocessed) Enhancers
19. (reprocessed)DPI_clustering

2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "FANTOM5" data.
File	README_e.html (English)

2.2 HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation

Data name	HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
Description of data contents	Time course and snapshot data by HeliScopeCAGE "basic" directory contains the following:   Subdirectories with "CAGEScan" in end (only human) 00_.assay_sdrf.txt: Experimental information for each sample (tab-delimited text) *.bam: Binary read mapping results (BAM format) *.bam.bai: Indexes of BAM files *.3prime.fq.gz: 3' sequences in CAGEscan tags (FASTQ format) *.5prime.fq.gz: 5' sequences in CAGEscan tags (FASTQ format) *.clusters.bed.gz Clustering results with CAGEscan (standard BED12 format). 4th column shows the CAGE tag name that represents the cluster and 5th column shows the number of pairs that constitute the cluster. *.pairs.bed.gz Read pairs mapped with CAGEscan (standard BED12 format). 4th column shows the pair's name and 5th column shows the total mapping quality value of reads.   Subdirectories expect above 00_.assay_sdrf.txt: Experimental information for each sample (tab-delimited text) *.bam: Binary read mapping results (BAM format) *.bam.bai: Indexes of BAM files *.ctss.bed.gz: TSS (CTSS) identified by CAGE tag analysis (BED format) *.rdna.fa.gz: rDNA sequences (FASTA format)
File	fantom5_new_experimental_details.zip (273 KB) basic (2.5 TB)

Data items are the following:

Data item	Description
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

2.3 CAGE peaks

Data name	CAGE peaks
Description of data contents	Data about CAGE peak regions and RNA transcriptional initiation activities measured by CAGE
File	CAGE_peaks (4.1 GB)

2.4 Pathway enrichment and co-expression cluster analysis

Data name	Pathway enrichment and co-expression cluster analysis
Description of data contents	Pathway enrichment and co-expression cluster analysis
File	Co-expression_clusters (86 MB)

2.5 Enhancers

Data name	Enhancers
Description of data contents	Human and mouse enhancers identified by measuring RNA transcripts amount with CAGE in phase1.0 and phase2.0
File	Enhancers (160 MB)

2.6 Results of de-novo and Motif activity analyses

Data name	Results of de-novo and Motif activity analyses
Description of data contents	Analysis results of TFBS motif near TSS de-novo motif analysis with HOMER etc. Significance of the correlation between transcriptional activations mesured by CAGE and de-novo motif/known TFBS motif (registered in JASPAR)
File	Motifs (6.2 GB)

2.7 CAGE_peaks_annotation

Data name	CAGE_peaks_annotation
Description of data contents	Annotation of human and mouse CAGE peaks and RNA transcriptional initiation activities by CAGE
File	CAGE_peaks_annotation (195 MB)

2.8 Sample ontology, GOstat and ontology term enrichment

Data name	Sample ontology, GOstat and ontology term enrichment
Description of data contents	The ontology to express samples in phase2.0 It is based on Cell Ontology, Disease Ontology and Pan-vertebrate Uberon Ontology. The file format is OBO.
File	Ontology (1.8 MB)

2.9 CAGE peaks identified as true TSS by TSS classifier

Data name	CAGE peaks identified as true TSS by TSS classifier
Description of data contents	Evaluation of CAGE peaks It shows that the sequence close to CAGE peak has "TSS-like" or not. "TSS_human.bed.gz" and "TSS_mouse.bed.gz" contain identified TSS.
File	TSS_classifier (32 MB)

2.10 (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation

Data name	(reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
Description of data contents	Time course and snapshot data by HeliScopeCAGE Human and mouse reads are re-mapped to new reference genome sequences (hg38/mm10). "basic" directory contains the following:   00_.assay_sdrf.txt: Experimental information for each sample (tabbed text) *.bam: Binary read mapping results (BAM format) *.bam.bai: Indexes of BAM files *.ctss.bed.gz: TSS (CTSS) identified by CAGE tag analysis (BED format) *.rdna.fa.gz: rDNA sequences (FASTA format)
File	fantom5_rp_exp_details.zip (237 KB) (reprocessed)basic (Homo sapiens) (1.4 TB) (reprocessed)basic (Mus musculus) (889 GB)

Data items are the following:

Data item	Description
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)

2.11 (reprocessed)CAGE peaks

Data name	(reprocessed)CAGE peaks
Description of data contents	Data about CAGE peak regions and RNA transcriptional initiation activities measured by CAGE. Human and mouse reads are re-mapped to new reference genome sequences (hg38/mm10).
File	(reprocessed)CAGE_peaks (Homo sapiens) (11 MB) (reprocessed)CAGE_peaks (Mus musculus) (8.1 MB)

2.12 (reprocessed)CAGE_peaks_annotation

Data name	(reprocessed)CAGE_peaks_annotation
Description of data contents	Annotation of human and mouse CAGE peaks and RNA transcriptional initiation activities by CAGE Human and mouse reads are re-mapped for new reference sequences (hg38/mm10).
File	(reprocessed)CAGE_peaks_annotation (Homo sapiens) (19 MB) (reprocessed)CAGE_peaks_annotation (Mus musculus) (14 MB)

2.13 (reprocessed)CAGE_peaks_expression

Data name	(reprocessed)CAGE_peaks_expression
Description of data contents	Annotation of human and mouse CAGE peaks and RNA transcriptional initiation activities by CAGE Human and mouse reads are re-mapped for new reference sequences (hg38/mm10).
File	(reprocessed)CAGE_peaks_annotation (Homo sapiens) (16 MB) (reprocessed)CAGE_peaks_annotation (Mus musculus) (13 MB)

2.14 (reprocessed)pooled_ctss

Data name	(reprocessed)pooled_ctss
Description of data contents	Mapping results of the all CAGE tags used from phase1.0 to phase2.0 Human and mouse reads are re-mapped for new reference sequences (hg38/mm10).
File	Mapping results of the all CAGE tags used from phase1.0 to phase2.0 Human and mouse reads in phase2.0 are re-mapped for new reference sequences (hg38/mm10). (6.5 GB) (reprocessed)pooled_ctss (Mus musculus) (4.5 GB)

2.15 DRA_accession_tables

Data name	DRA_accession_tables
Description of data contents	Accession number list of FANTOM5 sample data registered in DRA (http://trace.ddbj.nig.ac.jp/dra/index.html).
File	fantom5_dra_accession_tables.zip (64 KB) DRA_accession_tables (251KB)

Data items are the following:

Data item	Description
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

2.16 Gene_level_expression

Data name	Gene_level_expression
Description of data contents	Those tables shows the number of CAGE tags mapped on the same gene in each sample (human/mouse). The "counts" tables mean simple tabulation of tags and the "tpm" tables mean "TPM" (Transcripts Per Million) with RLE (Relative Log Expression).
File	gene_level_expression (415MB)

2.17 Summary_CAGEScan

Data name	Summary_CAGEScan
Description of data contents	The summary of CAGEscan experiments assembled in every DNA sequence library
File	fantom5_summary_cagescan.zip (4.64 KB) Summary_CAGEScan (62KB)

Data items are the following:

Data item	Description
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

2.18 (reprocessed) Enhancers

Data name	(reprocessed) Enhancers
Description of data contents	Identified enhancers of human and mouse by RNA transcription mesurement with CAGE. They are reprocessed with new reference genome sequences (hg38/mm10).
File	(reprocessed) enhancer (Homo sapiens) (101MB) (reprocessed) enhancer (Mus musculus) (7.3MB)

2.19 (reprocessed)DPI_clustering

Data name	(reprocessed)DPI_clustering
Description of data contents	This is the peak identification of human and mouse reprocessed mapping data with DPI (Decomposition-based peak identification) method. (BED format) *.tc.bed.gz: CAGE tag clusters with original definition *.tc.decompose_smoothing_merged.bed.gz: All peaks with DPI *.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz: All extracted peaks *.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz: Probable extracted peaks
File	(reprocessed)DPI_clustering (Homo sapiens) (150MB) (reprocessed)DPI_clustering (Mus musculus) (124MB)

3. License

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

4. Update History

Date	Update contents
2019/03/29	Archive V3 is released. The following data are added. 「DRA_accession_tables」 「Gene_level_expression」 「Summary_CAGEScan 」 「(reprocessed)Enhancers」 「(reprocessed)DPI_clustering」 The following data are updated. 「HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation」 「(reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation」 「CAGE peaks」 「(reprocessed)CAGE peaks」 「(reprocessed)CAGE_peaks_annotation」 「(reprocessed)CAGE_peaks_expression」 「(reprocessed)pooled_ctss」 「Enhancers」 「Sample ontology, GOstat and ontology term enrichment」
2017/03/14	FANTOM5 English archive site is opened.
2016/12/20	Archive V2 is released. The following data are added. (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation (reprocessed)CAGE peaks CAGE_peaks_annotation (reprocessed)CAGE_peaks_annotation (reprocessed)CAGE_peaks_expression (reprocessed)pooled_ctss The following data are updated. HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation CAGE peaks
2015/12/07	FANTOM5 archive site is opened. (Archive V1)
2014/03/27	FANTOM5 (http://fantom.gsc.riken.jp/5/) is opened.

5. Literature

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.
A promoter-level mammalian expression atlas.
Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.
PMID: 24670764

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.
An atlas of active enhancers across human cell types and tissues.
Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787.
PMID: 24670763

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.
PMID: 25678556

Chung-Chau Hon, Jordan A. Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J. L. Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M. Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A. Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A. Medvedeva, Alison C. Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A. Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O. Daub, Michiel J. L. de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci & Alistair R. R. Forrest
An atlas of human long non-coding RNAs with accurate 5' ends
Nature volume 543, pages 199–204 (09 March 2017)
PMID: 28241135

Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, The FANTOM Consortium, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest & Michiel J L de Hoon
An integrated expression atlas of miRNAs and their promoters in human and mouse
Nature Biotechnology volume 35, pages 872–878 (2017)
PMID: 28829439

6. Contact address

When you have any question about "FANTOM5", contact the following:

E-mail: fantom-help[at]riken[dot]jp