Coexpression cluster:C1339

Full id: C1339_small_colon_signet_trachea_gall_adenocarcinoma_Renal

Phase1 CAGE Peaks

Hg19::chr11:2925001..2925048,-	p4@SLC22A18AS
Hg19::chr3:168991226..168991244,-	p@chr3:168991226..168991244 -
Hg19::chr6:31846768..31846780,-	p1@SLC44A4
Hg19::chr9:130877529..130877536,-	p@chr9:130877529..130877536 -
Hg19::chr9:130877564..130877577,-	p@chr9:130877564..130877577 -
Hg19::chr9:130877614..130877619,-	p@chr9:130877614..130877619 -

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 of stomach	3.44e-07	3

Uber Anatomy

Ontology term	p-value	n
gastrointestinal system	5.14e-38	25
intestine	1.75e-30	17
large intestine	1.29e-20	11
subdivision of digestive tract	1.99e-20	118
digestive system	1.48e-18	145
digestive tract	1.48e-18	145
primitive gut	1.48e-18	145
endoderm-derived structure	1.21e-17	160
endoderm	1.21e-17	160
presumptive endoderm	1.21e-17	160
lower digestive tract	2.87e-15	5
colon	2.13e-13	9
rectum	5.71e-11	4
organ system subdivision	1.27e-10	223
gut epithelium	1.30e-09	54
small intestine	1.67e-09	4
stomach	2.11e-09	8
food storage organ	2.11e-09	8
digestive tract diverticulum	7.76e-09	23
multi-tissue structure	3.21e-08	342
hindgut	3.27e-08	19
epithelium of foregut-midgut junction	4.97e-08	25
anatomical boundary	4.97e-08	25
hepatobiliary system	4.97e-08	25
foregut-midgut junction	4.97e-08	25
septum transversum	4.97e-08	25
adult organism	9.54e-08	114
sac	1.04e-07	26
gland	5.37e-07	59
anatomical cluster	7.25e-07	373
hepatic diverticulum	8.04e-07	22
liver primordium	8.04e-07	22

Disease

Ontology term	p-value	n
signet ring cell adenocarcinoma	9.41e-11	2
gastrointestinal system cancer	5.38e-08	14

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	11.2315872630044	0.00159345997118423	0.0100391727049834
BHLHE40#8553	3	22.4359067734887	0.000210319610478028	0.00244632696277032
FOSL2#2355	3	8.46510030228085	0.00359831563461509	0.0182199401999208
FOXA1#3169	3	5.54070987469273	0.0119217877786028	0.0433757043654241
FOXA2#3170	3	12.3152318763326	0.00121971244012452	0.0082046597664669
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287461708090371
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318832956536012
HDAC2#3066	3	6.70781011831313	0.00697394002796266	0.0294855203052543
HNF4A#3172	3	11.5661451814768	0.00146348715008573	0.0093764268736767
HNF4G#3174	3	14.3767112632234	0.000776977293719738	0.00608981100028486
RXRA#6256	3	10.0373085695666	0.00220541911678922	0.0127051556698301
SMARCA4#6597	2	52.2553011026293	0.000599565921574195	0.00500944522266299
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472412094307865
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.0464013487871712
USF2#7392	3	6.4960986925348	0.00763431981530056	0.0314537349477366

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.