Data source

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) and its annotation
  • https:://...

• CAGE peak expression
  • https:://...

• Co expression cluster
  • https:://...

• GO enrichment analysis
  • https:://...

• Sample enrichment analysis
  • https:://...

Co expression cluster

• CP member list
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt

• Sample ontology enrichment analysis
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment_on_MCL_coexp_cluster_120516/

• GOstat analysis
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/gostat_analysis/go_all

• KEGG enrichment
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx

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
  • /work/arner/f5_mara/tf_networks_120418/tf_network/hg19/
  • 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
  • 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

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