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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
  • Ontology-based sample term enrichment analysis
https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/
<!-- ** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01_ontology_term_enrichment_1st/ -->

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

Gene

  • EntrezGene
https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz
  • Transcription factors
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz

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_June_25_2012.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
  • TF expression and enrichment table on FF sample page
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz

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/
  • Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term
https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/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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