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Coexpression cluster:C1694

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Full id: C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial



Phase1 CAGE Peaks

Hg19::chr12:95510642..95510668,-p@chr12:95510642..95510668
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Hg19::chr12:95510716..95510730,-p3@FGD6
Hg19::chr12:95510743..95510753,-p8@FGD6
Hg19::chr15:71389222..71389244,+p3@THSD4
Hg19::chr9:114908292..114908313,-p13@SUSD1


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


GO IDGO nameFDR corrected p-value
GO:0032488Cdc42 protein signal transduction0.0219815772092478
GO:0043088regulation of Cdc42 GTPase activity0.0219815772092478
GO:0032489regulation of Cdc42 protein signal transduction0.0219815772092478
GO:0032319regulation of Rho GTPase activity0.0219815772092478
GO:0046847filopodium formation0.028616528426325
GO:0030035microspike biogenesis0.028616528426325
GO:0030027lamellipodium0.028616528426325
GO:0022603regulation of anatomical structure morphogenesis0.028616528426325
GO:0008360regulation of cell shape0.028616528426325
GO:0022604regulation of cell morphogenesis0.028616528426325
GO:0001726ruffle0.028616528426325
GO:0030031cell projection biogenesis0.0304958262052178
GO:0031252leading edge0.0405097317596002
GO:0031267small GTPase binding0.0443909858229263
GO:0051020GTPase binding0.0472640384308379



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 cell1.74e-34253
endo-epithelial cell2.85e-2342
general ecto-epithelial cell2.84e-2014
respiratory epithelial cell9.80e-1713
endodermal cell1.34e-1558
gingival epithelial cell3.00e-123
squamous epithelial cell3.15e-1263
epithelial cell of Malassez4.67e-123
epidermal cell2.01e-109
stratified squamous epithelial cell3.34e-106
keratin accumulating cell3.34e-106
stratified epithelial cell3.34e-106
keratinizing barrier epithelial cell3.34e-106
epithelial fate stem cell3.34e-106
stratified epithelial stem cell3.34e-106
surface ectodermal cell3.34e-106
ecto-epithelial cell5.41e-0934
transitional epithelial cell5.63e-094
urothelial cell5.63e-094
sebum secreting cell9.95e-092
epithelial cell of sweat gland9.95e-092
epithelial cell of skin gland9.95e-092
acinar cell of sebaceous gland9.95e-092
mammary gland epithelial cell1.04e-084
epithelial cell of alimentary canal7.77e-0820
keratinocyte2.22e-075
epithelial cell of tracheobronchial tree8.99e-079
epithelial cell of lower respiratory tract8.99e-079
Uber Anatomy
Ontology termp-valuen
gingival epithelium3.00e-123
epithelial bud4.44e-1137
endoderm-derived structure2.96e-10160
endoderm2.96e-10160
presumptive endoderm2.96e-10160
epithelial fold1.00e-0947
endo-epithelium1.16e-0982
mouth mucosa1.80e-0913
jaw skeleton3.86e-094
splanchnocranium3.86e-094
skin gland9.95e-092
epidermis gland9.95e-092
gland of integumental system9.95e-092
sebaceous gland9.95e-092
skin sebaceous gland9.95e-092
sweat gland9.95e-092
sweat gland placode9.95e-092
sebaceous gland placode9.95e-092
mammary gland1.04e-084
mammary bud1.04e-084
mammary ridge1.04e-084
mammary placode1.04e-084
respiratory system1.34e-0874
surface structure1.48e-0899
mucosa6.87e-0820
primary subdivision of cranial skeletal system2.22e-075
urothelium2.99e-075
respiratory system epithelium4.72e-0728
respiratory tract6.84e-0754
Disease
Ontology termp-valuen
squamous cell carcinoma1.37e-1814
carcinoma3.70e-11106
clear cell adenocarcinoma6.77e-082
cell type cancer6.07e-07143


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
MEF2A#4205311.24593854578640.001399366787411950.00910185388992442
RAD21#588536.21302033727380.007751055068811640.0318894008403238
RFX5#599337.228746496317060.00502918278958660.0234651010258057
STAT3#677448.415571997723390.0003771527211598630.00374175482523178



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.