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Revision as of 17:23, 3 July 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)
- http://www.swissregulon.unibas.ch/
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/
FF Ontology
- https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/
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) , annotation, and expression
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
Sample enrichment analysis
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/

Co expression cluster

Gene

Motifs

SwissRegulon (known)
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon

Sample information

sample name and attributes
- https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_March15.xls
GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go

Ontology

Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
- https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FF_ontology_v019_01/

Network

MARA netwrok
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Network/mara_network

FANTOM5 BioMart

CAGE peak annotation

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
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.TATA_CpG_annotated.osc.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.full_set.TATA_CpG_annotated.osc.gz

Machine learning classification as TSS-like or not (KAUST)
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/tc.decompose_smoothing_merged.permissive_peaks_pos.bed.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/mm9.permissive_dpi_cluster.pos.bed.gz

T. Lassmann tss-like classifier (score):
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_human.bed.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_mouse.bed.gz

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

Relative expression
- hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_DPI_score_20120515/DPI_cluster_scores_human_june4.txt.gz
- mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_DPI_score_20120515/DPI_cluster_scores_mouse_may14.txt.gz

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