Data source: Difference between revisions
From FANTOM5_SSTAR
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=== | === MCL co expression === | ||
* CP member list | * CP member list | ||
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt] | ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt] | ||
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* KEGG enrichment | * KEGG enrichment | ||
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx] | ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx] | ||
* TFBS overrepresentation for the novel motifs | |||
** Human: https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/hg19.coexpression_clusters_overrepresentation.txt.bz2 | |||
** Mouse: https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/mm9.coexpression_clusters_overrepresentation.txt.bz2 | |||
=== Gene === | === Gene === |
Revision as of 13:20, 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
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
- MARA netwrok
FANTOM5 BioMart
CAGE peak annotation
- CAGE peak location (with the permissive threshold) and its association with genes