Coexpression cluster:C3432

Full id: C3432_pharyngeal_signet_serous_bile_rectal_clear_mucinous

Phase1 CAGE Peaks

Hg19::chr14:54317486..54317491,-	p4@ENST00000418927
Hg19::chr14:54317508..54317523,-	p2@ENST00000418927
Hg19::chr14:54317532..54317552,-	p1@ENST00000418927

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	4.03e-17	253
mesothelial cell	3.58e-14	19
endodermal cell	1.92e-10	58
cortical cell of adrenal gland	1.07e-08	2
metabolising cell	4.70e-07	12
endopolyploid cell	4.70e-07	12
parenchymal cell	4.70e-07	12
polyploid cell	4.70e-07	12
hepatocyte	4.70e-07	12

Uber Anatomy

Ontology term	p-value	n
gut epithelium	9.06e-17	54
endo-epithelium	2.67e-15	82
epithelium of foregut-midgut junction	5.91e-15	25
anatomical boundary	5.91e-15	25
hepatobiliary system	5.91e-15	25
foregut-midgut junction	5.91e-15	25
septum transversum	5.91e-15	25
biliary system	4.22e-14	9
biliary tree	4.22e-14	9
biliary bud	4.22e-14	9
epithelial sac	3.45e-12	25
sac	1.21e-11	26
hepatic diverticulum	2.00e-11	22
liver primordium	2.00e-11	22
digestive system	5.53e-11	145
digestive tract	5.53e-11	145
primitive gut	5.53e-11	145
digestive tract diverticulum	7.41e-11	23
endoderm-derived structure	2.81e-10	160
endoderm	2.81e-10	160
presumptive endoderm	2.81e-10	160
endocrine system	3.61e-10	45
bile duct	6.28e-10	6
digestive system duct	6.28e-10	6
endocrine gland	8.92e-10	35
subdivision of digestive tract	4.44e-09	118
abdomen element	4.23e-08	54
abdominal segment element	4.23e-08	54
trunk region element	6.38e-08	101
immaterial anatomical entity	3.59e-07	117
gland	4.14e-07	59
abdominal segment of trunk	5.07e-07	60
abdomen	5.07e-07	60

Disease

Ontology term	p-value	n
carcinoma	1.20e-22	106
cell type cancer	2.02e-17	143
cancer	9.84e-17	235
disease of cellular proliferation	3.51e-16	239
disease of anatomical entity	2.06e-12	39
endocrine gland cancer	5.47e-10	6
adenocarcinoma	2.45e-08	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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115056987649153
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167181420456976
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00896058332887245
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580374423224121
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107159516855797
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390586145086422
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122663372112809
JUND#3727	3	6.99466394187103	0.00292184504273499	0.015643336977403
MAFF#23764	3	56.3153564899452	5.59409009993116e-06	0.000168953492176608
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000857006568959921
PRDM1#639	3	131.830955777461	4.35536935195671e-07	2.07988303497488e-05
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024594058767828
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612474720908206

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.