Coexpression cluster:C3586

Full id: C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary

Phase1 CAGE Peaks

Hg19::chr16:68771187..68771201,+	p1@CDH1
Hg19::chr5:68711023..68711075,+	p2@MARVELD2
Hg19::chr5:68711076..68711103,+	p3@MARVELD2

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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GO ID	GO name	FDR corrected p-value
GO:0030054	cell junction	0.00429571419202788
GO:0044459	plasma membrane part	0.0299164706866183
GO:0005923	tight junction	0.0299164706866183
GO:0043296	apical junction complex	0.0299164706866183
GO:0016327	apicolateral plasma membrane	0.0299164706866183
GO:0050954	sensory perception of mechanical stimulus	0.0299164706866183
GO:0007605	sensory perception of sound	0.0299164706866183
GO:0005911	intercellular junction	0.0340594182494116
GO:0007156	homophilic cell adhesion	0.0340594182494116
GO:0005886	plasma membrane	0.0340594182494116
GO:0016337	cell-cell adhesion	0.0498875417599653

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	6.20e-26	254
endodermal cell	2.99e-17	59
endo-epithelial cell	5.47e-15	43
epithelial cell of alimentary canal	4.50e-08	21
respiratory epithelial cell	2.07e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	6.12e-22	169
endoderm	6.12e-22	169
presumptive endoderm	6.12e-22	169
adult organism	4.69e-17	115
digestive system	5.34e-17	155
digestive tract	5.34e-17	155
primitive gut	5.34e-17	155
subdivision of digestive tract	9.15e-16	129
endodermal part of digestive tract	9.15e-16	129
endo-epithelium	2.04e-14	82
mixed endoderm/mesoderm-derived structure	1.56e-13	130
immaterial anatomical entity	4.88e-12	126
trunk region element	1.12e-11	107
organ	1.01e-10	511
foregut	4.74e-10	98
respiratory system	9.28e-10	72
anatomical space	1.71e-09	104
gland	6.18e-09	59
epithelial bud	8.40e-09	37
organ part	1.52e-08	219
subdivision of trunk	6.28e-08	113
thoracic segment organ	1.25e-07	35
thoracic cavity element	1.77e-07	34
thoracic cavity	1.77e-07	34
epithelial fold	2.87e-07	51
lung	3.45e-07	22
respiratory tube	3.45e-07	22
respiration organ	3.45e-07	22
pair of lungs	3.45e-07	22
lung primordium	3.45e-07	22
lung bud	3.45e-07	22
multi-tissue structure	4.63e-07	347
respiratory tract	5.83e-07	53
gut epithelium	6.50e-07	54

Disease

Ontology term	p-value	n
carcinoma	1.60e-20	106
cell type cancer	1.32e-12	143
squamous cell carcinoma	1.12e-08	14
adenocarcinoma	2.57e-07	25

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	2	14.9754496840058	0.00576829454079388	0.0259535978608466
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294064528175555
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329805451951252
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457331822933716
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541934317856543
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190015604924905
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421246791887293
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242489963260739

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.