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** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_human.bed.gz]
** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_human.bed.gz]
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_mouse.bed.gz]
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_mouse.bed.gz]
* Annotation
** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.GencodeV10_annotated.osc.gz GencodeV10]
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.permissive_set.Ensembl_annotated.osc.gz Ensembl]
* Repeat Annotation
** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.robust_set.Repeat_annotated.sym.osc]
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.robust_set.Repeat_annotated.sym.osc]


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

Revision as of 10:55, 7 February 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