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* CpG island and TATA-box annotation
* CpG island and TATA-box annotation
** https:://...
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.TATA_CpG_annotated.osc.gz


* Machine learning classification as TATA-like or not (KAUST)
* Machine learning classification as TATA-like or not (KAUST)
** https:://...
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/tc.decompose_smoothing_merged.permissive_peaks_pos.bed.gz


=== CAGE peak expression (for the ones with the robust threshold) ===
=== CAGE peak expression (for the ones with the robust threshold) ===

Revision as of 10:49, 12 June 2012

Data sources used in the database(s)


old info on the top page


FANTOM5 Resource Browser

CAGE peaks

  • CAGE peak location (with the robust threshold) and its annotation
    • https:://...
  • CAGE peak expression
    • https:://...
  • Co expression cluster
    • https:://...
  • GO enrichment analysis
    • https:://...
  • Sample enrichment analysis
    • https:://...

Gene

  • EntrezGene
    • https:://...
  • Transcription factors
    • https:://...

Motifs

  • SwissRegulon (known)
    • https:://...
  • de novo motifs (HOMER)
    • https:://...

Sample information

  • sample name
    • phase1 freeze https:://...
  • sample attributes
    • Marina's excel? https:://...
  • sample ontology
    • FF ontology v6 https:://...

Network

  • MARA netwrok
    • FF ontology v6 https:://...

FANTOM5 BioMart

CAGE peak annotation (for the ones with the permissive threshold)

CAGE peak expression (for the ones with the robust threshold)

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