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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte
|full_id=C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte
|id=C2089
|id=C2089

Revision as of 14:45, 12 September 2012


Full id: C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:101980713..101980754,+p8@YAP1
Hg19::chr11:101981327..101981348,+p7@YAP1
Hg19::chr11:101981353..101981380,+p5@YAP1
Hg19::chr11:101981423..101981503,+p3@YAP1


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
non-terminally differentiated cell3.77e-13180
fibroblast9.90e-1075
epithelial cell1.76e-08254
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.00e-16169
endoderm1.00e-16169
presumptive endoderm1.00e-16169
multi-tissue structure1.87e-15347
digestive system3.83e-15155
digestive tract3.83e-15155
primitive gut3.83e-15155
mesenchyme5.08e-15238
entire embryonic mesenchyme5.08e-15238
multi-cellular organism1.65e-13659
trunk9.24e-12216
mixed endoderm/mesoderm-derived structure6.67e-11130
organism subdivision5.42e-10365
subdivision of digestive tract1.01e-09129
endodermal part of digestive tract1.01e-09129
organ component layer3.40e-0957
organ3.83e-09511
reproductive structure4.98e-0959
reproductive system4.98e-0959
primordium5.79e-09168
surface structure8.72e-0995
embryo1.55e-08612
trunk mesenchyme2.25e-08143
anatomical system2.46e-08625
anatomical group3.48e-08626
larynx1.18e-079
organ part3.64e-07219
reproductive organ3.66e-0748
orifice5.15e-0735
embryonic structure5.65e-07605
developing anatomical structure5.65e-07605
germ layer9.97e-07604
embryonic tissue9.97e-07604
presumptive structure9.97e-07604
epiblast (generic)9.97e-07604
Disease
Ontology termp-valuen
cell type cancer1.68e-09143
carcinoma2.25e-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
BHLHE40#8553222.43590677348870.002891464496853120.0156361860190982
E2F4#187439.501045236463330.001850751034728270.010923457887312
EP300#203335.08045629466740.01144298405398240.0418655437404143
GABPB1#255335.300762877136630.01012678824234270.0378360690173517
GATA3#2625320.42738726790450.0001924415576258320.00231868987504433
HEY1#2346244.040111043105710.00375304636917980.0185475043652472
MAX#414934.839416631755340.01315737137836840.0465874257318082
STAT3#677437.889598747865680.003190760481680130.0167373095904667
TAF1#687243.343046285745290.008005664898701650.0321158345377392
TCF7L2#693438.077632422353010.002978381685834620.0158558061416496
TFAP2A#7020416.5186343730451.34240829060362e-050.00032581868338915
TFAP2C#7022410.80922860986027.32289634782688e-050.00114336368914739
TRIM28#10155418.59052504526258.36730015875654e-060.000229664247379862



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.