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Genes, TSS regions, motifs, samples, etc profiled in FANTOM5.

Usage

• Just click any in the left menue
• Or, keyword search on top of this page.
• Or, make a complex query at Special:Ask, if you are familiar with Semantic MediaWIki

Note

• we are focusing on phase1 freeze, and we are still keep updating this.
• expression view on genes are little bit slow now. We are now investigating alternative ways.
• contact: KAWAJI, Hideya <kawaji@gsc.riken.jp>, SHIMOJI, Hisashi <hisashi.shimoji@dnaform.jp>, or WP4 <fantom5-wp4@gsc.riken.jp>

Data source

• CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
• Swissregulon motifs, and Motif Activity Response Analysis (MARA)
  • http://www.swissregulon.unibas.ch/
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/
• FF Ontology
  • https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/
• facet classification based on FF ontology
  • http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)

Other browsers/resources

• FANTOM5 collaboration wiki
• zenbu
• UCSC mirror (at RIKEN)
• FONSE (Fantomy ONtology Sample Explorer) (user:terry , pass: T34s377)
• BioLayout

• phase1 data freeze
• latest update