Main Page

What's new

• FANTOM5 short RNA analysis
• UPDATE_023 is released (January 14th, 2014)
• UPDATE_022 is released (December 10th, 2012)
• UPDATE_020 is released (August 17th, 2012)
• UPDATE_019 is released (June 19th, 2012)
• UPDATE_018 is released (June 1st, 2012)
• UPDATE_017 is released (Mar 26th, 2012)
• Phase 1 Freeze configurations are available for pooled samples. See ZENBU_Config page.
• UCSC Genome Browser mirror is continuously updated. New major functions become available - "track search" to find dataset with keywords, and "track hubs" to load external data (now Roadmap Epigenomic data can be shown via this function) (21st Sep, 2011)
• UPDATE_013 is released. See File_release (21st Sep, 2011)
• FANTOM5 ontology v5 covering all the update12 samples is provided by Terry Meehan (8th Sep, 2011)
• Resource Wiki is opened (Aug 5th, 2011)
• The same snapshot of UCSC database files has been copied (find "2011-06-20" directory under each genome assembly) (19th July, 2011)
• gene expression files on UPDATE_012 are available (11th July, 2011)
• gene/promoter coordinates of the UCSC/ENCODE snapshot (20th June, 2011) has been prepared (6th July, 2011)
• UPDATE_012 is released. See File_release (4th July, 2011)
• Recent snapshot of UCSC/ENCODE (20th June, 2011) has been taken in UCSC RIKEN mirror (4th July, 2011)
• Clusters uploaded ( Last update: June 1, 2011) sample config
• UPDATE_011 with gene expression
• Data availability
• Wiki is up! [March 17, 2011]
• News archives

FANTOM5 - five dimensions of cellular identity

Welcome to the FANTOM5 collaborator website. In FANTOM5 we are expanding the efforts made in FANTOM3 and 4 and aim to generate both a map of the majority of human promoters and comparative models of transcriptional regulatory network models of each cellular state. To achieve this we are carrying out deepCAGE sequencing on the Heliscope true single molecule sequencer on RNA isolated from every major human organ, over 200 cancer cell lines, 30 time courses of cellular differentiation, mouse developmental time courses and over 200 primary cell types

For those new to the FANTOM collaboration, please take some time to read the introductory material FANTOM5_overview.

FANTOM5 Main papers

• Promoterome paper
• Time-courses main paper
• Long noncoding RNA main paper (obsolete)
• FANTOM CAT lncRNA paper

FANTOM5 Satellite papers

Satellite papers

The first FANTOM5 meeting in February 2011

We are planning to have the first of two FANTOM5 meetings in February 2011(Feb 20-25th). All participants will have an opportunity to present and attendants will be asked to submit an abstract by February 10. More information

Collected samples, sample annotations, and data production status

This summary of samples and data production will be updated monthly. It details which samples are completed, scheduled or not yet scheduled. Please look here before emailing about sample scheduling. Sample annotations are also included.

• File:Helicos data production schedule November 2014.xls
• File:CAGEscan production schedule April04 2012.xls
• File:Short RNA Production schedule April04 2012.xls - 336 libraries (mostly primary cells) with matching helicos CAGE data
• File:ShortRNA Phase2 timecourse 2012.xls - 120 libraries (mostly 7 timecourses, snapshots for B-cells and Hepatocytes)
• File:RNAseq HiSeq production schedule April04 2012.xls

• Working draft of cell ontology update File:CELL ONTOLOGY FANTOM5 Feb2011.xls

Data Analysis and Integration (WP5)

Please put your data analysis results into this section Data Analysis and Integration.

Current sections

Mapping and QC / Clustering , peak calling / Expression normalization and differential expression (based on genes, peaks, or whatever) / Annotation of promoter , 'gene' expression / Motif activity / Conservation , orthologous mapping (variome, basins) / Main paper specific analysis

Resources

Data files

All the data produced in the FANTOM5 collaboration will be shared by any of the FANTOM5 collaborators to encourage a wide range of analysis with following the FANTOM5 rules. Please note that all the data is confidential and don't share with other people before public release. Please read FANTOM5_overview for the project plan.

All the data is accessible from share directory, and Dataset_introduction and File_release would be helpful to understand the data contents and the situation of the release.

Genome Browser

The FANTOM5 data is visible on two genome browsers, ZENBU (developed in RIKEN OSC, this allow us to manipulate data in a flexible way) and a local mirror of the UCSC Genome Browser.

• ZENBU Homepage. See ZENBU_Config for all the pre-configured views. See also ZENBU_Howto, ZENBU_wishlist, and ZENBU_administration.
• UCSC_Local_Mirror

Additional information

• FANTOM5_overview
• Dataset_introduction
• File_release
• Category:Methods_and_Protocols
• Sample documentation
• Platform evaluation project

RSS/Atom feed

An good alternative to checking the wiki pages regularly to keep up-to-date with additions and modifications to all the FANTOM5 wiki page is to subscribe to the RSS feed of the "Recent Change" special page by clicking on  or :

1. Go to "Recent Change"
   
2. The bottom right toolbox provide links to RSS or Atom feed
3. Choose your favorite RSS/Atom reader and stay up-to-date with all the modifications to any page or page additons

Contacts/Mailing lists

Open for all FANTOM5 members

• fantom5@gsc.riken.jp (all FANTOM5 members; in principle, here is the place for discussion)
  • A list of all collaborators can be viewed from the bottom of this page: FANTOM5_overview
• fantom5-wp5@gsc.riken.jp (WP5 is data analysis/integration work package; see Work packages; the place for bioinformatics related details)
• fantom5-samples@gsc.riken.jp (the place for sample related discussion - mainly sample annotation at this moment)

Each mailing list can have a different administrator. To be added to a specific mailing list, please email to: list_you_want_to_be_added_to-admin@gsc.riken.jp . The requests will be redirected to the person who's in charge of that mailing list administration.

Examples:

• fantom5-wp5@gsc [Data analysis] email to fantom5-wp5-admin@gsc.riken.jp
• fantom5-samples@gsc email to fantom5-samples-admin@gsc.riken.jp (or, directly, to m.lizio@gsc.riken.jp)

Related but limited to RIKEN members

• fantom5-secretariat@gsc.riken.jp (FANTOM5 secretariat)
• fantom5-wp4@gsc.riken.jp (data control work package, 4). Any questions about Wiki, File Servers, Genome Browser, etc.
• fantom5_enquiries@gsc.riken.jp ; for non-FANTOM5 member to contact us. http://fantom.gsc.riken.jp/5/

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Note: you can create your own account on this wiki freely. See the corner of top-right. Alternatively, you can use 'oscf5', with the same password to access here.