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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4813_Urothelial_Bronchial_Small_Prostate_Fibroblast_tubular_lens
|full_id=C4813_Urothelial_Bronchial_Small_Prostate_Fibroblast_tubular_lens
|id=C4813
|id=C4813

Revision as of 17:57, 12 September 2012


Full id: C4813_Urothelial_Bronchial_Small_Prostate_Fibroblast_tubular_lens



Phase1 CAGE Peaks

Hg19::chr9:21591738..21591749,-p@chr9:21591738..21591749
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Hg19::chr9:21591753..21591793,-p@chr9:21591753..21591793
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Hg19::chr9:21591797..21591817,-p@chr9:21591797..21591817
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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>


Uber Anatomy
Ontology termp-valuen
artery1.48e-1342
arterial blood vessel1.48e-1342
arterial system1.48e-1342
multilaminar epithelium3.40e-1382
systemic artery1.00e-1133
systemic arterial system1.00e-1133
blood vessel4.62e-1160
epithelial tube open at both ends4.62e-1160
blood vasculature4.62e-1160
vascular cord4.62e-1160
vasculature7.27e-1179
vascular system7.27e-1179
vessel3.23e-1069
dermomyotome5.95e-1070
somite6.05e-1083
paraxial mesoderm6.05e-1083
presomitic mesoderm6.05e-1083
presumptive segmental plate6.05e-1083
trunk paraxial mesoderm6.05e-1083
presumptive paraxial mesoderm6.05e-1083
unilaminar epithelium1.78e-09138
anatomical system1.92e-09625
skeletal muscle tissue2.02e-0961
striated muscle tissue2.02e-0961
myotome2.02e-0961
anatomical group2.59e-09626
epithelium4.42e-09309
cell layer7.30e-09312
muscle tissue1.10e-0863
musculature1.10e-0863
musculature of body1.10e-0863
splanchnic layer of lateral plate mesoderm1.15e-0884
multi-cellular organism4.11e-08659
aorta5.90e-0821
aortic system5.90e-0821
cardiovascular system1.30e-07110
organism subdivision3.27e-07365
epithelial tube3.51e-07118
circulatory system5.85e-07113
Disease
Ontology termp-valuen
reproductive organ cancer5.38e-0829
female reproductive organ cancer1.14e-0727
ovarian cancer1.81e-0714
squamous cell carcinoma7.39e-0714


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#105137.971147625824820.001974187055288560.0115897763837707
EP300#203336.77394172622320.003216880500103790.016864159348978
FOS#235338.99795530889440.001372499272417130.00902603434997623
FOSL2#2355316.93020060456170.0002060162053171620.00244196191886495
GATA2#2624312.7449317335540.0004829527704283790.00439365020825518
GTF2F1#2962312.73966087675770.0004835525047438590.00436262439901036
JUN#3725312.51282919233630.0005103313992726250.00446647959512559
JUND#372736.994663941871030.002921845042734990.0157808643749392
MAFF#23764356.31535648994525.59409009993116e-060.000169394368207222
MAFK#7975327.10073313782995.02195559325033e-050.000859816426563068
MXI1#460139.96157162875930.001011470541259020.00724036818770055
NR3C1#2908314.9730233311730.0002978331194675480.00310619064949783
RAD21#5885310.35503389545630.0009004912073565420.00669512359970882
RFX5#5993312.04791082719510.0005717246050312580.00486994095301032
SMARCC1#6599343.66335931963151.20046018043203e-050.000302764696411835
SMC3#9126315.04493284493280.0002935825420371870.00311157571623927
STAT3#6774310.51946499715420.0008589184530415310.00646240071444453
TCF7L2#6934310.77017656313730.0008003181298398380.00618045143170237
TFAP2A#7020316.5186343730450.0002218033880766340.00249810460987119
TFAP2C#7022310.80922860986020.0007916746575753130.00619617128016398
USF1#739136.361499277207960.00388404057290560.0191369209507802



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.