Data source: Difference between revisions
From FANTOM5_SSTAR
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** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples Human] | ** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples Human] | ||
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples_mm9 Mouse] | ** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples_mm9 Mouse] | ||
* [http://fantom.gsc.riken.jp/5/datafiles/ | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression] | ||
* [http://fantom.gsc.riken.jp/5/datafiles/ | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs] | ||
* Repeat family, relative expression | * Repeat family, relative expression | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human] | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse] | ||
=== Ontology === | === Ontology === | ||
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)] | * [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)] | ||
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term] | * [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term] | ||
Revision as of 16:58, 12 February 2015
Data sources used in FANTOM5 SSTAR
CAGE peaks
- CAGE peak location (with the robust threshold) , annotation, and expression
- Ontology-based sample term enrichment analysis
Genes
- Gene details (obtained from EntrezGene)
Coexpression module
- FFCP member list
- Sample ontology enrichment analysis
- GOStat results on Coexpression module
- Pathway enrichment analysis
- TFBS overrepresentation
- ENCODE_TF_ChIP-seq_peak enrichment analysis
- Relative expression of the co-expression module
Motifs
- Novel motifs GREAT analysis results
- Novel motifs Significance of the correlation with CAGE expression
- Jaspar motifs Significance of the correlation with CAGE expression
Sample
- sample name and attributes
- Transcription factors, relative expression
- HOMER motifs
- Repeat family, relative expression
