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* CAGE peak location (with the permissive threshold) and its association with genes
* CAGE peak location (with the permissive threshold) and its association with genes
** https:://...
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
** mm9:
 
* CAGE peak location (with the robust threshold) and its association with genes
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz
** mm9:
 
* CAGE peak descriptions
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz
** mm9:


* CpG island and TATA-box annotation
* CpG island and TATA-box annotation
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* Machine learning classification as TATA-like or not (KAUST)
* Machine learning classification as TATA-like or not (KAUST)
** https:://...
** https:://...


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

Revision as of 10:44, 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)

  • CpG island and TATA-box annotation
    • https:://...
  • Machine learning classification as TATA-like or not (KAUST)
    • https:://...

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

  • Counts
    • https:://...
  • TPM (RLE normalization-based)
    • https:://...
  • Relative expression
    • https:://...