Coexpression cluster:C4569

Full id: C4569_placenta_mesothelioma_liposarcoma_rectal_prostate_Intestinal_adrenal

Phase1 CAGE Peaks

Hg19::chr6:142623708..142623713,+	p8@GPR126
Hg19::chr6:142623784..142623795,+	p5@GPR126
Hg19::chr6:142623806..142623820,+	p2@GPR126

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-38	254
endodermal cell	1.04e-16	59
endo-epithelial cell	3.01e-12	43
squamous epithelial cell	3.01e-12	62
mesothelial cell	6.65e-10	19
epithelial cell of alimentary canal	4.82e-07	21
respiratory epithelial cell	6.39e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.09e-32	169
endoderm	1.09e-32	169
presumptive endoderm	1.09e-32	169
subdivision of digestive tract	1.57e-26	129
endodermal part of digestive tract	1.57e-26	129
digestive system	2.98e-26	155
digestive tract	2.98e-26	155
primitive gut	2.98e-26	155
mixed endoderm/mesoderm-derived structure	5.24e-25	130
foregut	5.62e-19	98
endo-epithelium	2.86e-17	82
respiratory system	2.03e-13	72
trunk region element	2.84e-12	107
organ	7.73e-12	511
respiratory tract	8.21e-12	53
gland	9.67e-12	59
multi-tissue structure	3.45e-11	347
immaterial anatomical entity	4.01e-11	126
gut epithelium	4.29e-10	54
epithelial fold	1.39e-09	51
epithelial bud	3.22e-09	37
mesenchyme	7.68e-09	238
entire embryonic mesenchyme	7.68e-09	238
respiratory primordium	7.75e-09	38
endoderm of foregut	7.75e-09	38
primordium	8.00e-09	168
organ part	9.25e-09	219
segment of respiratory tract	2.21e-08	46
orifice	2.22e-08	35
multi-cellular organism	4.85e-08	659
exocrine gland	1.06e-07	31
exocrine system	1.06e-07	31
sac	1.51e-07	26
organism subdivision	2.35e-07	365
anatomical system	2.61e-07	625
subdivision of trunk	2.62e-07	113
anatomical space	2.90e-07	104
organ segment	2.97e-07	97
epithelial sac	3.16e-07	25
anatomical group	3.38e-07	626
anatomical cluster	4.58e-07	286
epithelium of foregut-midgut junction	6.87e-07	25
anatomical boundary	6.87e-07	25
hepatobiliary system	6.87e-07	25
foregut-midgut junction	6.87e-07	25
septum transversum	6.87e-07	25

Disease

Ontology term	p-value	n
carcinoma	1.79e-21	106
cell type cancer	4.38e-17	143
squamous cell carcinoma	8.39e-08	14
cancer	1.61e-07	235
disease of anatomical entity	1.96e-07	39
disease of cellular proliferation	8.24e-07	239

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115689665507396
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327353059450372
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016826152278777
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058368529884151
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107621695918021
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00085430170873053
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295820349782445
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00618412188201257

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.