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=== CAGE peaks ===
=== CAGE peaks ===
* CAGE peak location (with the robust threshold) , annotation, and expression
* CAGE peak location (with the robust threshold) , annotation, and expression
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/CAGE_peaks/hg19.cage_peak_tpm_ann.osc.txt.gz Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/hg19.cage_peak_tpm_ann.osc.txt.gz Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/CAGE_peaks/mm9.cage_peak_tpm_ann.osc.txt.gz Mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_tpm_ann.osc.txt.gz Mouse]
* Ontology-based sample term enrichment analysis
* Ontology-based sample term enrichment analysis
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]
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=== Genes ===
=== Genes ===
* Transcription factors (curated list)
* 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/phase2.0/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]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]


* Gene details (obtained from EntrezGene)
* Gene details (obtained from EntrezGene)
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=== Coexpression module ===
=== Coexpression module ===
* FFCP member list
* FFCP member list
** [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/phase2.0/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]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/sstar/coexpression_module/ffcp_member_list/mouse_filtered2_p75_m22_T.clusters.txt Mouse]
* Sample ontology enrichment analysis
* Sample ontology enrichment analysis
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]
* GOStat results on Coexpression module
* GOStat results on Coexpression module
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]
* Pathway enrichment analysis
* Pathway enrichment analysis
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]
* TFBS overrepresentation
* TFBS overrepresentation
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif]
** [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]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz human_jaspar_motif]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]
** [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/phase2.0/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]
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/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
* 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/phase2.0/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]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse]


=== Motifs ===
=== Motifs ===
* Novel motifs GREAT analysis results
* Novel motifs GREAT analysis results
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]
* Novel motifs Significance of the correlation with CAGE expression
* Novel motifs Significance of the correlation with CAGE expression
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]
* Jaspar motifs Significance of the correlation with CAGE expression
* Jaspar motifs Significance of the correlation with CAGE expression
** [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/phase2.0/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]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]


=== Sample ===
=== Sample ===
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** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples Human]
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples Human]
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples_mm9 Mouse]
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples_mm9 Mouse]
* [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Transcription_factors/ Transcription factors, relative expression]
* [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/ HOMER motifs]
* Repeat family, relative expression
* Repeat family, relative expression
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]


=== Ontology ===
=== Ontology ===
* [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)]
* [http://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)]
* [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]

Revision as of 09:51, 9 February 2015

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

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