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{{#ask:[[Category:motif]]
 
|?#
Data sources used in FANTOM5 SSTAR
|?Name
 
|format=broadtable
 
|offset=0
=== CAGE peaks ===
|limit=500
* CAGE peak location (with the robust threshold) , annotation, and expression
|mainlabel=
** <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>
|class=sortable wikitable smwtable
** <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
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
** <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>
 
* Gene details (obtained from EntrezGene)
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
 
=== Coexpression module ===
* FFCP member list
** <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
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
** <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
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
** <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
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
** <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
** <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>
** <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>
** <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>
** <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 ===
* Novel motifs GREAT analysis results
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
** <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
** <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>
** <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 ===
* sample name and attributes
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
* Repeat family, relative expression
** <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>
** <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 ===
* <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>
* <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 20:55, 16 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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