Data source

Data sources used in the database(s)

FANTOM5 Resource Browser

CAGE peaks

• CAGE peak location (with the robust threshold) , annotation, and expression
  • [1]
  • [2]
• Ontology-based sample term enrichment analysis
  • [3]

Transcription Factors

• TF entrezgene list
  • hg19: [4]
  • mm9: [5]

MCL co expression

• CP member list
  • [6]
• Sample ontology enrichment analysis
  • [7]
• GOstat analysis
  • [8]
• KEGG enrichment
  • [9]
• TFBS overrepresentation for the novel motifs
  • hg19: [10]
  • mm9: [11]

Gene

• EntrezGene detail information
  • [12]
  • [13]

Motifs

• MacroAPE_1083: Position weight matrices and p-value for sample specificity
  • [14]
• TomTom analysis results for MacroAPE_1083 motifs
  • [15]
• SwissRegulon (known)
  • [16]

• Position Weight Matrices of novel motifs

• P-values for novel motifs for the human samples

• P-values for novel motifs for the mouse samples

• P-values for known JASPAR motifs for human samples

• P-values for known JASPAR motifs for mouse samples

• Co-expression clusters overrepresentation for known JASPAR motifs for human

• Co-expression clusters overrepresentation for known JASPAR motifs for mouse

Sample information

• sample name and attributes
  • [17]
• GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
  • [18]
• TF expression and enrichment table on FF sample page
  • [19]
  • [20]
  • [21]
  • [22]
• Top motif activities with MARA (same value imported in Swissregulon pages)
  • [23]
  • [24]

Ontology

• Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
  • [25]
• Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term
  • [26]

Network

• MARA netwrok
  • [27]

FANTOM5 BioMart

CAGE peak annotation

• CAGE peak location (with the permissive threshold) and its association with genes
  • hg19: tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
  • mm9: tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz

• CAGE peak location (with the robust threshold) and its association with genes
  • hg19: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz
  • mm9: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz

• CAGE peak descriptions
  • hg19: tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz
  • mm9: tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz

• CpG island and TATA-box annotation
  • hg19: DPIcluster_hg19_20120116.permissive_set.TATA_CpG_annotated.osc.gz
  • mm9: DPIcluster_mm9_20120116.full_set.TATA_CpG_annotated.osc.gz

• Machine learning classification as TSS-like or not (KAUST)
  • hg19: tc.decompose_smoothing_merged.permissive_peaks_pos.bed.gz
  • mm9: mm9.permissive_dpi_cluster.pos.bed.gz

• T. Lassmann tss-like classifier (score):
  • hg19: TSS_human.bed.gz
  • mm9: TSS_mouse.bed.gz

• Association
  • hg19: DPIcluster_hg19_20120116.permissive_set.GencodeV10_annotated.osc.gz
  • mm9: DPIcluster_mm9_20120116.permissive_set.Ensembl_annotated.osc.gz

• Repeat Annotation
  • hg19: DPIcluster_hg19_20120116.robust_set.Repeat_annotated.sym.osc
  • mm9: DPIcluster_mm9_20120116.robust_set.Repeat_annotated.sym.osc

Sample Names and IDs

• Sample Names and IDs (Phase 1.0)
  • 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): hg19.cage_peak_tpm.osc.txt.gz
  • mm9: 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: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.sync015.clustername_update.osc.txt.gz
  • mm9: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.counts.selected.clustername_update.osc.txt.gz

• TPM (RLE normalization-based)
  • hg19: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
  • mm9: tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz

• Relative expression
  • hg19: DPI_cluster_scores_human_june4.txt.gz
  • mm9: DPI_cluster_scores_mouse_may14.txt.gz