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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4610_amniotic_immature_cervical_chorionic_Gingival_nasal_epidermoid
|full_id=C4610_amniotic_immature_cervical_chorionic_Gingival_nasal_epidermoid
|id=C4610
|id=C4610

Revision as of 17:43, 12 September 2012


Full id: C4610_amniotic_immature_cervical_chorionic_Gingival_nasal_epidermoid



Phase1 CAGE Peaks

Hg19::chr6:47666275..47666296,+p3@GPR115
Hg19::chr6:47666310..47666332,+p1@GPR115
Hg19::chr6:47666342..47666355,+p4@GPR115


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 cell2.31e-21254
endo-epithelial cell1.39e-1843
endodermal cell1.54e-1359
respiratory epithelial cell1.25e-0913
epithelial cell of alimentary canal3.46e-0921
squamous epithelial cell2.34e-0862
embryonic cell1.73e-07248
Uber Anatomy
Ontology termp-valuen
female organism4.08e-1441
endoderm-derived structure1.01e-13169
endoderm1.01e-13169
presumptive endoderm1.01e-13169
reproductive structure2.75e-1359
reproductive system2.75e-1359
female reproductive organ1.53e-1237
female reproductive system1.53e-1237
extraembryonic membrane6.16e-1114
membranous layer6.16e-1114
reproductive organ2.96e-1048
orifice3.84e-0935
digestive system4.41e-09155
digestive tract4.41e-09155
primitive gut4.41e-09155
mixed endoderm/mesoderm-derived structure9.19e-09130
subdivision of digestive tract1.83e-08129
endodermal part of digestive tract1.83e-08129
endo-epithelium2.14e-0882
respiratory system8.44e-0872
female gonad9.57e-0813
chorion1.46e-077
immaterial anatomical entity5.42e-07126
anatomical space5.62e-07104
epithelial bud8.18e-0737
respiratory tract9.95e-0753
Disease
Ontology termp-valuen
ovarian cancer1.55e-1014
reproductive organ cancer3.74e-0929
squamous cell carcinoma4.67e-0914
female reproductive organ cancer2.08e-0827
carcinoma3.68e-08106


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
CEBPB#105137.971147625824820.001974187055288560.0115741619999597
EP300#203336.77394172622320.003216880500103790.0168312099869916
FOS#235338.99795530889440.001372499272417130.00901468156166106
GTF2F1#2962312.73966087675770.0004835525047438590.0043584827861348
JUN#3725312.51282919233630.0005103313992726250.00446236612597402
JUND#372736.994663941871030.002921845042734990.0157604882976035
MYC#460935.22228187160940.007020843755740150.0295880034301407
NR3C1#2908314.9730233311730.0002978331194675480.0031006173409162
STAT3#6774310.51946499715420.0008589184530415310.0064531029650532
TRIM28#10155318.59052504526250.0001555969297255280.00198006430408241
USF1#739136.361499277207960.00388404057290560.0191071744415303
USF2#7392312.99219738506960.0004558979393427810.00422893017914741



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.