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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2630_extraskeletal_Fibroblast_Smooth_Aortic_mesothelioma_prostate_small
|full_id=C2630_extraskeletal_Fibroblast_Smooth_Aortic_mesothelioma_prostate_small
|id=C2630
|id=C2630

Revision as of 15:23, 12 September 2012


Full id: C2630_extraskeletal_Fibroblast_Smooth_Aortic_mesothelioma_prostate_small



Phase1 CAGE Peaks

Hg19::chr21:38071403..38071428,+p2@SIM2
Hg19::chr21:38071430..38071456,+p1@SIM2
Hg19::chr21:38071462..38071474,+p3@SIM2
Hg19::chr21:38071488..38071502,+p4@SIM2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell2.12e-15254
Uber Anatomy
Ontology termp-valuen
mesenchyme3.06e-16238
entire embryonic mesenchyme3.06e-16238
multi-tissue structure6.70e-13347
trunk1.38e-10216
trunk region element7.47e-09107
trunk mesenchyme4.02e-08143
organism subdivision7.04e-08365
digestive system7.87e-08155
digestive tract7.87e-08155
primitive gut7.87e-08155
mixed endoderm/mesoderm-derived structure1.08e-07130
intermediate mesoderm1.67e-0737
endoderm-derived structure2.20e-07169
endoderm2.20e-07169
presumptive endoderm2.20e-07169
immaterial anatomical entity2.74e-07126
kidney3.32e-0727
kidney mesenchyme3.32e-0727
kidney rudiment3.32e-0727
kidney field3.32e-0727
anatomical space3.52e-07104
foregut4.21e-0798
segment of respiratory tract5.71e-0746
subdivision of digestive tract6.15e-07129
endodermal part of digestive tract6.15e-07129
urinary system structure9.21e-0744
Disease
Ontology termp-valuen
cell type cancer1.04e-31143
carcinoma2.17e-29106
cancer5.94e-23235
disease of cellular proliferation2.71e-21239
adenocarcinoma3.62e-1225


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F6#187645.017155731697390.00157802193473060.00997681656524783
EGR1#195844.988179094810140.001615011500076050.0101516813756511
MXI1#460149.96157162875930.0001015224754950450.00142531332413321
MYC#460945.22228187160940.001344309395272740.00888428329639242
SUZ12#23512450.11578091106291.5827390373096e-078.82539681353859e-06
TAF1#687243.343046285745290.008005664898701650.0322620634494329
USF1#739146.361499277207960.0006105011399140830.00508413432353775
ZNF263#1012748.221841637010680.0002187871180958320.00249235469315124



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.