Data source: Difference between revisions
From FANTOM5_SSTAR
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* CAGE peak location (with the permissive threshold) and its association with genes | * CAGE peak location (with the permissive threshold) and its association with genes | ||
** https:://... | ** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz | ||
** mm9: | |||
* CAGE peak location (with the robust threshold) and its association with genes | |||
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz | |||
** mm9: | |||
* CAGE peak descriptions | |||
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz | |||
** mm9: | |||
* CpG island and TATA-box annotation | * CpG island and TATA-box annotation | ||
| Line 76: | Line 85: | ||
* Machine learning classification as TATA-like or not (KAUST) | * Machine learning classification as TATA-like or not (KAUST) | ||
** https:://... | ** https:://... | ||
=== CAGE peak expression (for the ones with the robust threshold) === | === CAGE peak expression (for the ones with the robust threshold) === | ||
Revision as of 10:44, 12 June 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.
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
- Swissregulon motifs, and Motif Activity Response Analysis (MARA)
- FF Ontology
- facet classification based on FF ontology
- http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)
FANTOM5 Resource Browser
CAGE peaks
- CAGE peak location (with the robust threshold) and its annotation
- https:://...
- CAGE peak expression
- https:://...
- Co expression cluster
- https:://...
- GO enrichment analysis
- https:://...
- Sample enrichment analysis
- https:://...
Gene
- EntrezGene
- https:://...
- Transcription factors
- https:://...
Motifs
- SwissRegulon (known)
- https:://...
- de novo motifs (HOMER)
- https:://...
Sample information
- sample name
- phase1 freeze https:://...
- sample attributes
- Marina's excel? https:://...
- sample ontology
- FF ontology v6 https:://...
Network
- MARA netwrok
- FF ontology v6 https:://...
FANTOM5 BioMart
CAGE peak annotation (for the ones with the permissive threshold)
- 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
- https:://...
- Machine learning classification as TATA-like or not (KAUST)
- https:://...
CAGE peak expression (for the ones with the robust threshold)
- Counts
- https:://...
- TPM (RLE normalization-based)
- https:://...
- Relative expression
- https:://...
