Coexpression cluster:C1534

Full id: C1534_gastric_signet_endometrial_pharyngeal_papillotubular_bile_squamous

Phase1 CAGE Peaks

Hg19::chr7:116312178..116312192,+	p7@MET
Hg19::chr7:116312193..116312211,+	p5@MET
Hg19::chr7:116312213..116312230,+	p3@MET
Hg19::chr7:116312243..116312256,+	p2@MET
Hg19::chr7:116312277..116312288,+	p8@MET
Hg19::chr7:116312308..116312319,+	p9@MET

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	1.52e-39	254
endo-epithelial cell	7.30e-12	43
endodermal cell	1.31e-11	59
embryonic cell	5.18e-11	248
squamous epithelial cell	3.24e-09	62

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.09e-17	169
endoderm	2.09e-17	169
presumptive endoderm	2.09e-17	169
anatomical system	4.40e-14	625
anatomical group	5.13e-14	626
digestive system	9.93e-14	155
digestive tract	9.93e-14	155
primitive gut	9.93e-14	155
mixed endoderm/mesoderm-derived structure	1.11e-13	130
multi-cellular organism	6.81e-13	659
subdivision of digestive tract	9.99e-13	129
endodermal part of digestive tract	9.99e-13	129
organ	1.12e-11	511
mesenchyme	8.79e-11	238
entire embryonic mesenchyme	8.79e-11	238
multi-tissue structure	9.47e-11	347
organ part	9.55e-10	219
respiratory primordium	1.57e-09	38
endoderm of foregut	1.57e-09	38
embryonic structure	2.17e-09	605
developing anatomical structure	2.17e-09	605
embryo	3.24e-09	612
germ layer	3.54e-09	604
embryonic tissue	3.54e-09	604
presumptive structure	3.54e-09	604
epiblast (generic)	3.54e-09	604
foregut	5.08e-09	98
respiratory tract	6.73e-09	53
endo-epithelium	1.51e-08	82
respiratory system	2.07e-08	72
trunk region element	2.36e-08	107
organism subdivision	5.28e-08	365
epithelium	2.56e-07	309
cell layer	4.76e-07	312
extraembryonic membrane	7.77e-07	14
membranous layer	7.77e-07	14
epithelial fold	8.57e-07	51
epithelial bud	9.99e-07	37

Disease

Ontology term	p-value	n
carcinoma	2.05e-18	106
cell type cancer	4.62e-17	143
adenocarcinoma	1.11e-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
BHLHE40#8553	6	44.8718135469774	1.22070649245094e-10	1.31161898523748e-08
CTCF#10664	6	5.36025637307503	4.21437267579784e-05	0.000756262659600774
E2F1#1869	6	4.90738921487932	7.15746523583771e-05	0.00112798930400733
E2F6#1876	6	5.01715573169739	6.26776799983417e-05	0.00102521444343724
EGR1#1958	6	4.98817909481014	6.48943962979974e-05	0.00105552185873953
EP300#2033	6	6.7739417262232	1.03454107484288e-05	0.000270048576144752
FOS#2353	6	8.9979553088944	1.88302066097805e-06	6.94669003221076e-05
JUND#3727	6	6.99466394187103	8.53468650061654e-06	0.00023242610780649
MAX#4149	6	6.45255550900712	1.3848964723355e-05	0.000334730855529386
MXI1#4601	6	9.9615716287593	1.02262624227062e-06	4.3047989567312e-05
MYC#4609	6	5.2222818716094	4.92821127172503e-05	0.00085469521256674
NR3C1#2908	6	14.973023331173	8.86442195171695e-08	5.24825036403269e-06
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380744956256576
RAD21#5885	6	10.3550338954563	8.10515055094479e-07	3.54626652027701e-05
SMC3#9126	6	15.0449328449328	8.61317699636729e-08	5.12857236216421e-06
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573827594210693
TCF7L2#6934	6	10.7701765631373	6.40204410218762e-07	2.91593146091745e-05
TFAP2A#7020	6	16.518634373045	4.91595718330683e-08	3.16143874548881e-06
TFAP2C#7022	6	10.8092286098602	6.2644941908553e-07	2.8670355337368e-05
USF1#7391	6	6.36149927720796	1.50818327938273e-05	0.000357091710531519
USF2#7392	6	12.9921973850696	2.07721573629339e-07	1.11423900504748e-05

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.