Data source: Difference between revisions
From FANTOM5_SSTAR
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** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse] | ** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse] | ||
* Ontology-based sample term enrichment analysis | * Ontology-based sample term enrichment analysis | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human] | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse] | ||
=== Genes === | === Genes === | ||
* Transcription factors (curated list) | * Transcription factors (curated list) | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human] | ||
** [http://fantom.gsc.riken.jp/5/datafiles/ | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse] | ||
* Gene details (obtained from EntrezGene) | * Gene details (obtained from EntrezGene) | ||
Revision as of 16:49, 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
