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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3035_prostate_signet_epidermoid_Keratinocyte_giant_Mammary_mucinous
|full_id=C3035_prostate_signet_epidermoid_Keratinocyte_giant_Mammary_mucinous
|id=C3035
|id=C3035

Revision as of 15:53, 12 September 2012


Full id: C3035_prostate_signet_epidermoid_Keratinocyte_giant_Mammary_mucinous



Phase1 CAGE Peaks

Hg19::chr10:6779293..6779312,+p4@ENST00000417112
Hg19::chr10:6779326..6779351,+p3@ENST00000417112
Hg19::chr10:6779369..6779400,+p1@ENST00000417112


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 cell1.32e-33254
endo-epithelial cell4.28e-1143
squamous epithelial cell1.71e-0962
epithelial cell of nephron8.16e-0816
kidney cell1.53e-0718
kidney epithelial cell1.53e-0718
kidney tubule cell2.66e-0712
nephron tubule epithelial cell2.66e-0712
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.43e-19169
endoderm6.43e-19169
presumptive endoderm6.43e-19169
multi-tissue structure9.96e-16347
respiratory system2.27e-1572
organ part8.93e-15219
digestive system5.72e-13155
digestive tract5.72e-13155
primitive gut5.72e-13155
respiratory tract1.19e-1153
mesenchyme2.81e-11238
entire embryonic mesenchyme2.81e-11238
segment of respiratory tract5.88e-1146
urinary system structure1.90e-1044
mixed endoderm/mesoderm-derived structure2.53e-10130
organ3.36e-10511
renal system5.72e-1045
respiratory primordium9.19e-1038
endoderm of foregut9.19e-1038
organism subdivision2.96e-09365
anatomical space5.34e-09104
extraembryonic membrane8.07e-0914
membranous layer8.07e-0914
subdivision of head1.44e-0848
mesonephros1.63e-0818
pronephros1.63e-0818
nephrogenic cord1.63e-0818
pronephric mesoderm1.63e-0818
rostral part of nephrogenic cord1.63e-0818
presumptive pronephric mesoderm1.63e-0818
orifice1.95e-0835
subdivision of digestive tract2.08e-08129
endodermal part of digestive tract2.08e-08129
intermediate mesoderm2.10e-0837
urogenital ridge2.60e-0820
excretory tube2.66e-0817
mesonephric epithelium2.66e-0817
mesonephric tubule2.66e-0817
nephric duct2.66e-0817
kidney epithelium2.66e-0817
renal duct2.66e-0817
mesonephric duct2.66e-0817
pronephric duct2.66e-0817
larynx2.84e-089
embryo2.84e-08612
organ segment5.75e-0897
multi-cellular organism7.55e-08659
nephron epithelium8.16e-0816
nephron8.16e-0816
uriniferous tubule8.16e-0816
metanephric mesenchyme8.16e-0816
nephrogenic mesenchyme8.16e-0816
foregut1.32e-0798
embryonic structure1.57e-07605
developing anatomical structure1.57e-07605
germ layer2.47e-07604
embryonic tissue2.47e-07604
presumptive structure2.47e-07604
epiblast (generic)2.47e-07604
immaterial anatomical entity2.52e-07126
renal tubule2.66e-0712
nephron tubule2.66e-0712
nephron tubule epithelium2.66e-0712
duct2.98e-0726
primordium3.07e-07168
trunk region element3.30e-07107
anatomical system3.72e-07625
anatomical group4.71e-07626
endo-epithelium5.48e-0782
Disease
Ontology termp-valuen
carcinoma1.53e-11106
squamous cell carcinoma1.77e-1114


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
EP300#203336.77394172622320.003216880500103790.0166791333242486
GTF2F1#2962312.73966087675770.0004835525047438590.00432637197318118
JUN#3725312.51282919233630.0005103313992726250.00443009733261023
JUND#372736.994663941871030.002921845042734990.0156113252375403
NR3C1#2908314.9730233311730.0002978331194675480.00307791343400666
RFX5#5993312.04791082719510.0005717246050312580.00482859016859612
STAT1#6772320.70658749719920.0001125992441046670.00154388242812752
STAT3#6774310.51946499715420.0008589184530415310.00641388419256431



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.

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