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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/phase2.0/extra/CAGE_peaks/hg19.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Human]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse]
** <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
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>


=== 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]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>


* Gene details (obtained from EntrezGene)
* Gene details (obtained from EntrezGene)
** [ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>


=== Coexpression module ===
=== Coexpression module ===
* FFCP member list
* FFCP member list
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mouse_filtered2_p75_m22_T.clusters.txt Mouse]
** <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
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
* 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]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]</span>
* 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]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]
** <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
* 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]
** <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>
** [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]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]
** <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>
** [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]
** <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>
* [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]
* <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
* Relative expression of the co-expression module
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz human]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse]
** <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 ===
* Novel motifs GREAT analysis results
* Novel motifs GREAT analysis results
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
* 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/phase2.0/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]
** <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
* Jaspar motifs Significance of the correlation with CAGE expression
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]
** <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 ===
=== Sample ===
* sample name and attributes
* sample name and attributes
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples Human]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
** [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Browse_samples_mm9 Mouse]
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Transcription_factors/ Transcription factors, relative expression]
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Motifs/ HOMER motifs]
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
* Repeat family, relative expression
* Repeat family, relative expression
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]
** <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>
** [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]
** <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>


=== Ontology ===
=== Ontology ===
* [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)]
* <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>
* [http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]</span>
 
=== CAGEd-oPOSSUM ===
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
* <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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