Data source: Difference between revisions
From FANTOM5_SSTAR
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** https: | ** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_DPI_score_20120515/DPI_cluster_scores_human_june4.txt.gz | ||
** mm9: | |||
Revision as of 10:47, 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
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
- 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: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz
- 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: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz
- 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
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.sync015.clustername_update.osc.txt.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.clustername_update.osc.txt.gz
- TPM (RLE normalization-based)
- hg19: 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
- mm9: 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
