Data source

Data sources used in the database(s)

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 classification

• sample name
  • phase1 freeze https:://...

• sample attributes
  • Marina's excel? https:://...

• sample ontology
  • FF ontology v6 https:://...

FANTOM5 BioMart

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

• CAGE peak location (with the permissive threshold) and its association with genes
  • https:://...

• 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:://...