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* SwissRegulon (known)
* SwissRegulon (known)
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon]
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon]
* [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/novel_pwms.txt Position Weight Matrices of novel motifs]


* [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/hg19.pvalues.txt P-values for novel motifs for the human samples]
* [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/hg19.pvalues.txt P-values for novel motifs for the human samples]

Revision as of 18:21, 23 January 2013

Data sources used in the database(s)


FANTOM5 Resource Browser

CAGE peaks

  • CAGE peak location (with the robust threshold) , annotation, and expression
  • Ontology-based sample term enrichment analysis

Transcription Factors

  • TF entrezgene list

MCL co expression

  • CP member list
  • Sample ontology enrichment analysis
  • GOstat analysis
  • KEGG enrichment
  • TFBS overrepresentation for the novel motifs

Gene

Motifs

  • MacroAPE_1083: Position weight matrices and p-value for sample specificity
  • TomTom analysis results for MacroAPE_1083 motifs
  • SwissRegulon (known)

Sample information

  • sample name and attributes
  • GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
  • TF expression and enrichment table on FF sample page
  • Top motif activities with MARA (same value imported in Swissregulon pages)

Ontology

  • Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
  • Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term

Network

FANTOM5 BioMart

CAGE peak annotation

  • CAGE peak location (with the permissive threshold) and its association with genes
  • CAGE peak location (with the robust threshold) and its association with genes
  • CAGE peak descriptions
  • CpG island and TATA-box annotation
  • Machine learning classification as TSS-like or not (KAUST)
  • T. Lassmann tss-like classifier (score):

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

  • TPM (RLE normalization-based)
  • Relative expression