|
|
| Line 1: |
Line 1: |
|
| |
|
| Data sources used in the database(s) | | Data sources used in FANTOM5 SSTAR |
|
| |
|
|
| |
| = 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] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/CAGE_peaks/hg19.cage_peak_tpm_ann.osc.txt.gz Human] |
| ** [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] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/CAGE_peaks/mm9.cage_peak_tpm_ann.osc.txt.gz Mouse] |
| * 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/] | | ** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human] |
| <!-- ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01_ontology_term_enrichment_1st/] -->
| | ** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse] |
| | |
| | === Genes === |
| | * Transcription factors (curated list) |
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human] |
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse] |
|
| |
|
| === Transcription Factors ===
| | * Gene details (obtained from EntrezGene) |
| * TF entrezgene list
| | ** [ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse] |
| ** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_official.xls]
| |
| ** mm9: [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] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/sstar/coexpression_module/ffcp_member_list/SYNC015_combined_clustertables.txt Human] |
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/sstar/coexpression_module/ffcp_member_list/mouse_filtered2_p75_m22_T.clusters.txt Mouse] |
| * 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/] | | ** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human] |
| * GOstat analysis | | ** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse] |
| ** [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 | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human] |
| ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse] |
| * TFBS overrepresentation for the novel motifs | | * Pathway enrichment analysis |
| ** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/hg19.coexpression_clusters_overrepresentation.txt.bz2] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human] |
| ** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/Novel/mm9.coexpression_clusters_overrepresentation.txt.bz2] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse] |
| | | * TFBS overrepresentation |
| === Gene ===
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif] |
| * EntrezGene detail information | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz human_jaspar_motif] |
| ** [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz]
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif] |
| ** [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz mouse_jaspar_motif] |
| | * [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] |
| | * Relative expression of the co-expression module |
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz human] |
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse] |
|
| |
|
| === 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/]
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human] |
| * TomTom analysis results for MacroAPE_1083 motifs
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse] |
| ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/ohmiya/F5_motifs/] | | * Novel motifs Significance of the correlation with CAGE expression |
| * SwissRegulon (known)
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human] |
| ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon]
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse] |
| | | * Jaspar motifs Significance of the correlation with CAGE expression |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/novel_pwms.txt Position Weight Matrices of novel motifs]
| | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human] |
| | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse] |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/hg19.pvalues.txt P-values for novel motifs for the human samples] | |
| | |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Novel/mm9.pvalues.txt P-values for novel motifs for the mouse samples] | |
| | |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/KNOWN_JASPAR_130/hg19.pvalues.txt P-values for known JASPAR motifs for human samples] | |
| | |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/KNOWN_JASPAR_130/mm9.pvalues.txt P-values for known JASPAR motifs for mouse samples] | |
| | |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/MacroAPE_20120919/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.bz2 Co-expression clusters overrepresentation for known JASPAR motifs for human] | |
| | |
| * [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/MacroAPE_20120919/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.bz2 Co-expression clusters overrepresentation for known JASPAR motifs for mouse] | |
|
| |
|
| === 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_April25_2013.xls] | | ** Human |
| * GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples | | ** Mouse |
| ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go]
| | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression] |
| * TF expression and enrichment table on FF sample page
| | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs] |
| ** [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] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human] |
| ** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz] | | ** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse] |
| ** [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) | | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/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/]
| | * [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term] |
| * 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 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 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 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 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 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 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 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 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 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 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 TSS_human.bed.gz]
| |
| ** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/Final/TSS_mouse.bed.gz TSS_mouse.bed.gz]
| |
| | |
| * Association
| |
| ** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.GencodeV10_annotated.osc.gz DPIcluster_hg19_20120116.permissive_set.GencodeV10_annotated.osc.gz]
| |
| ** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.permissive_set.Ensembl_annotated.osc.gz DPIcluster_mm9_20120116.permissive_set.Ensembl_annotated.osc.gz]
| |
| | |
| * Repeat Annotation
| |
| ** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.robust_set.Repeat_annotated.sym.osc DPIcluster_hg19_20120116.robust_set.Repeat_annotated.sym.osc]
| |
| ** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.robust_set.Repeat_annotated.sym.osc DPIcluster_mm9_20120116.robust_set.Repeat_annotated.sym.osc]
| |
| | |
| | |
| === Sample Names and IDs ===
| |
| | |
| * Sample Names and IDs
| |
| ** hg19 (Phase 1.0): [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 tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.sync015.clustername_update.osc.txt.gz]
| |
| ** hg19 (Phase 1.1): [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/hg19.cage_peak_tpm.osc.txt.gz hg19.cage_peak_tpm.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 tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.clustername_update.osc.txt.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 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 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 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 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 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 DPI_cluster_scores_mouse_may14.txt.gz]
| |
