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Data sources used in the database(s)
Data sources used in FANTOM5 SSTAR


== 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 peaks ===
* CAGE peak location (with the robust threshold) , annotation, and expression
* 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]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/hg19.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Human]</span>
** [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]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse]</span>
* Ontology-based sample term enrichment analysis
* Ontology-based sample term enrichment analysis
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
<!-- ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01_ontology_term_enrichment_1st/] -->
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>
 
=== Genes ===
* Transcription factors (curated list)
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>


=== Transcription Factors ===
* Gene details (obtained from EntrezGene)
* TF entrezgene list
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
** Human: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_official.xls]
** Mouse: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_official.xls]


=== MCL co expression ===
=== Coexpression module ===
* CP member list
* FFCP member list
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mouse_filtered2_p75_m22_T.clusters.txt Mouse]</span>
* Sample ontology enrichment analysis
* Sample ontology enrichment analysis
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment_on_MCL_coexp_cluster_120516/]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
* GOstat analysis
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/gostat_analysis/go_all]
* GOStat results on Coexpression module
* KEGG enrichment
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]</span>
* TFBS overrepresentation for the novel motifs
* Pathway enrichment analysis
** Human: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/hg19.coexpression_clusters_overrepresentation.txt.bz2]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
** Mouse: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/mm9.coexpression_clusters_overrepresentation.txt.bz2]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]</span>
 
* TFBS overrepresentation
=== Gene ===
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif]</span>
* EntrezGene detail information
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz human_jaspar_motif]</span>
** [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]</span>
** [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz  mouse_jaspar_motif]</span>
* <span class="plainlinks">[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/ENCODE_TF_ChIP-seq_peak_enrichment_coexprclusterencode.filtered.csv.gz ENCODE_TF_ChIP-seq_peak enrichment analysis]</span>
* Relative expression of the co-expression module
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse]</span>


=== Motifs ===
=== Motifs ===
* MacroAPE_1083: Position weight matrices and p-value for sample specificity
* Novel motifs GREAT analysis results
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/MacroAPE_1083/]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
* TomTom analysis results for MacroAPE_1083 motifs
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/ohmiya/F5_motifs/]
* Novel motifs Significance of the correlation with CAGE expression
* SwissRegulon (known)
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>
* Jaspar motifs Significance of the correlation with CAGE expression
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>


=== Sample information ===
=== Sample ===
* sample name and attributes
* sample name and attributes
** [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_June_25_2012.xls]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
* GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go]
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
* TF expression and enrichment table on FF sample page
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz]
* Repeat family, relative expression
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]</span>
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz]
* Top motif activities with MARA (same value imported in Swissregulon pages)
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/hg19/hg19.toptfs.txt.bz2]
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/mm9/mm9.toptfs.txt.bz2]


=== Ontology ===
=== Ontology ===
* Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)]</span>
** [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FF_ontology_v019_01/]
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]</span>
* 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
=== CAGEd-oPOSSUM ===
** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_DPI_score_20120515/DPI_cluster_scores_human_june4.txt.gz]
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_DPI_score_20120515/DPI_cluster_scores_mouse_may14.txt.gz]
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/index.html Mouse]</span>

Latest revision as of 09:44, 17 February 2022

Data sources used in FANTOM5 SSTAR


CAGE peaks

  • CAGE peak location (with the robust threshold) , annotation, and expression
  • Ontology-based sample term enrichment analysis

Genes

Coexpression module

Motifs

  • Novel motifs GREAT analysis results
  • Novel motifs Significance of the correlation with CAGE expression
  • Jaspar motifs Significance of the correlation with CAGE expression

Sample

Ontology

CAGEd-oPOSSUM

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