Coexpression cluster:C4636

Full id: C4636_squamous_oral_Hep2_epidermoid_mesothelioma_mucinous_ductal

Phase1 CAGE Peaks

Hg19::chr7:101917447..101917479,+	p4@CUX1
Hg19::chr7:101917482..101917507,+	p6@CUX1
Hg19::chr7:101917509..101917520,+	p9@CUX1

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

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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

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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>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.13e-31	254
endodermal cell	2.35e-10	59
endo-epithelial cell	5.59e-09	43
mesothelial cell	9.21e-08	19
squamous epithelial cell	3.86e-07	62
animal cell	7.51e-07	679
eukaryotic cell	7.51e-07	679

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	7.99e-19	169
endoderm	7.99e-19	169
presumptive endoderm	7.99e-19	169
digestive system	1.89e-17	155
digestive tract	1.89e-17	155
primitive gut	1.89e-17	155
subdivision of digestive tract	6.14e-16	129
endodermal part of digestive tract	6.14e-16	129
mixed endoderm/mesoderm-derived structure	4.29e-15	130
respiratory tract	1.13e-14	53
respiratory system	1.95e-14	72
segment of respiratory tract	2.53e-14	46
respiratory primordium	2.77e-14	38
endoderm of foregut	2.77e-14	38
larynx	4.51e-12	9
foregut	1.10e-11	98
immaterial anatomical entity	1.31e-09	126
endo-epithelium	3.58e-09	82
mesenchyme	4.99e-09	238
entire embryonic mesenchyme	4.99e-09	238
anatomical space	1.16e-08	104
upper respiratory tract	4.64e-08	19
mucosa	1.05e-07	12
thoracic cavity element	1.26e-07	34
thoracic cavity	1.26e-07	34
trunk region element	1.90e-07	107
reproductive structure	2.61e-07	59
reproductive system	2.61e-07	59
thoracic segment organ	3.02e-07	35
multi-tissue structure	5.64e-07	347
primordium	6.51e-07	168

Disease

Ontology term	p-value	n
carcinoma	9.68e-37	106
cell type cancer	3.38e-29	143
disease of cellular proliferation	6.15e-22	239
cancer	6.86e-21	235
squamous cell carcinoma	8.41e-13	14
adenocarcinoma	3.15e-10	25
disease of anatomical entity	3.68e-07	39
respiratory system cancer	7.94e-07	16

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00130004427126657
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115767614748614
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324166556358154
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322355208252314
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168371144908459
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000372540720638565
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00244057695861151
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123399172881884
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157629306481843
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187340574937036
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723144659491724
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295939742909047
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000606260024587833
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165970218441246
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247830527644191
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191089746275527
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00423005729273461
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.011008985090653

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

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This analysis result is provided for C0 - C305 clusters.