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Coexpression cluster:C4266: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4266_immature_thyroid_Small_smallcell_Renal_chorionic_pancreas
|full_id=C4266_immature_thyroid_Small_smallcell_Renal_chorionic_pancreas
|id=C4266
|id=C4266

Revision as of 17:19, 12 September 2012


Full id: C4266_immature_thyroid_Small_smallcell_Renal_chorionic_pancreas



Phase1 CAGE Peaks

Hg19::chr3:111805212..111805258,+p1@C3orf52
Hg19::chr3:111805262..111805289,+p2@C3orf52
Hg19::chr3:111805316..111805323,+p4@C3orf52


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 cell1.23e-26254
endo-epithelial cell6.43e-1243
embryonic cell6.98e-09248
endodermal cell1.29e-0859
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.13e-15169
endoderm3.13e-15169
presumptive endoderm3.13e-15169
digestive system2.41e-12155
digestive tract2.41e-12155
primitive gut2.41e-12155
anatomical space1.36e-11104
subdivision of digestive tract1.28e-10129
endodermal part of digestive tract1.28e-10129
mesenchyme5.40e-10238
entire embryonic mesenchyme5.40e-10238
anatomical cavity2.19e-0970
reproductive structure2.90e-0959
reproductive system2.90e-0959
immaterial anatomical entity3.83e-09126
female organism6.82e-0941
body cavity precursor9.90e-0963
mixed endoderm/mesoderm-derived structure1.72e-08130
endo-epithelium3.25e-0882
primordium3.83e-08168
respiratory system7.71e-0872
multi-tissue structure1.02e-07347
reproductive organ1.07e-0748
female reproductive organ1.09e-0737
female reproductive system1.09e-0737
respiratory tract3.08e-0753
trunk3.40e-07216
renal system5.82e-0745
epithelial bud6.17e-0737
epithelial fold6.37e-0751
body cavity7.85e-0746
urinary system structure8.23e-0744
Disease
Ontology termp-valuen
carcinoma9.26e-19106
cell type cancer3.16e-13143
reproductive organ cancer4.68e-0929
female reproductive organ cancer8.61e-0927
squamous cell carcinoma1.26e-0814
disease of cellular proliferation4.27e-08239
cancer3.36e-07235


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
E2F1#186934.907389214879320.008460985347239390.0326494309506867
E2F6#187635.017155731697390.00791769806886330.0323329997503036
MAX#414936.452555509007120.003721913834265510.0187034094662395
MXI1#460139.96157162875930.001011470541259020.00721613305953624
MYC#460935.22228187160940.007020843755740150.0295331843485478
PRDM1#6393131.8309557774614.35536935195671e-072.08369408955111e-05
TCF7L2#6934310.77017656313730.0008003181298398380.00615768566099476
YY1#752834.911170749853860.008441455341808260.0330280281138543
ZBTB7A#5134137.35190930787590.002516255860282270.0140584842343134



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.