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** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/]
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/]
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=== Transcription Factors
* TF entrezgene list
** Human: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_official.xls]
** Mouse: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_official.xls]


=== MCL co expression ===
=== MCL co expression ===

Revision as of 13:47, 26 November 2012

Data sources used in the database(s)


old info on the top page

  • CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
  • Swissregulon motifs, and Motif Activity Response Analysis (MARA)
  • FF Ontology
  • facet classification based on FF ontology
    • [6] FONSE (Fantomy ONtology Sample Explorer)


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