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=== Sample information ===
=== Sample information ===
* sample name and attributes
* sample name and attributes
** [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_June_25_2012.xls]
** [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_November07_2012.xls]
* GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
* GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go]
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go]

Revision as of 10:32, 26 December 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

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