FANTOM5

2017/03/14

Web Site: http://fantom.gsc.riken.jp/5/
FTP Site: ftp://ftp.biosciencedbc.jp/archive/fantom5/

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

README Content

Database Component
Data Description
License
Update History
Literature
Contact address

1. Database Component

README
HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
(reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation
CAGE peaks
(reprocessed)CAGE peaks
CAGE_peaks_annotation
(reprocessed)CAGE_peaks_annotation
(reprocessed)CAGE_peaks_expression
(reprocessed)pooled_ctss
Pathway enrichment and co-expression cluster analysis
Enhancers
Results of de-novo and Motif activity analyses
Sample ontology, GOstat and ontology term enrichment
CAGE peaks identified as true TSS by TSS classifier

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2. Data Description

2.1 README

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

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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: 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)

HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation

Time course and snapshot data by HeliScopeCAGE
"basic" directory contains the following:

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)

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)

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2.3 (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 in phase2.0 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)

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

Time course and snapshot data by HeliScopeCAGE
Human and mouse reads in phase2.0 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)

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)

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2.4 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)

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2.5 (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 in phase2.0 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)

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2.6 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)

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2.7 (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 in phase2.0 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)

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2.8 (reprocessed)CAGE_peaks_expression

Data name	(reprocessed)CAGE_peaks_expression
Description of data contents	Expression of human and mouse RNA transcriptional initiation activities by CAGE Human and mouse reads in phase2.0 are re-mapped for new reference sequences (hg38/mm10).
File	(reprocessed)CAGE_peaks_expression (Homo sapiens) (3.3 GB) (reprocessed)CAGE_peaks_expression (Mus musculus) (1.9 GB)

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2.9 (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 in phase2.0 are re-mapped for new reference sequences (hg38/mm10).
File	(reprocessed)pooled_ctss (Homo sapiens) (6.5 GB) (reprocessed)pooled_ctss (Mus musculus) (4.5 GB)

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2.10 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)

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2.11 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)

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2.12 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)

Results of de-novo and Motif activity analyses

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)

Motifs (6.2 GB)

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2.13 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)

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2.14 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)

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3. License

Last updated : 2017/03/14

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.

The license for this database is specified in the Creative Commons Attribution 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "FANTOM5 c RIKEN licensed under CC Attribution 4.0 International".

The summary of the Creative Commons Attribution 4.0 International is found here.

With regard to this database, you are licensed to:

freely access part or whole of this database, and acquire data;
freely redistribute part or whole of the data from this database; and
freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

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

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

Date	Update contents
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.

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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, Jorgensen 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, Muller 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, Drablos F, Lennartsson A, Ronnerblad 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

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6. Contact address

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

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

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