Coexpression cluster:C1459

Full id: C1459_rectum_colon_amniotic_Intestinal_small_chorionic_pancreatic

Phase1 CAGE Peaks

Hg19::chr19:959112..959138,+	p@chr19:959112..959138 +
Hg19::chr19:959145..959162,+	p@chr19:959145..959162 +
Hg19::chr7:100609502..100609528,+	p12@MUC3A p12@MUC3B
Hg19::chr7:100609529..100609542,+	p22@MUC3A p22@MUC3B
Hg19::chr7:100609612..100609625,+	p11@MUC3A p11@MUC3B
Hg19::chr7:100609627..100609654,+	p3@MUC3A p3@MUC3B

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
germ line cell	1.87e-17	7
germ cell	1.87e-17	7
embryonic stem cell	1.42e-13	5

Uber Anatomy

Ontology term	p-value	n
intestine	1.27e-17	17
gastrointestinal system	8.84e-16	25
large intestine	2.05e-12	11
lower digestive tract	9.77e-10	5
subdivision of digestive tract	2.62e-08	118
hindgut	2.83e-08	19
colon	4.82e-08	9
endoderm-derived structure	1.14e-07	160
endoderm	1.14e-07	160
presumptive endoderm	1.14e-07	160
rectum	3.02e-07	4

Disease

Ontology term	p-value	n
carcinoma	1.44e-08	106
cell type cancer	1.59e-07	143

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
CCNT2#905	6	6.33620157696263	1.54467812014647e-05	0.00036252727683141
CTCF#10664	4	3.57350424871668	0.0131663500723851	0.0466097361266975
CTCFL#140690	4	13.1643162393162	9.07806692187542e-05	0.00132435288623236
E2F4#1874	4	8.44537354352296	0.000511119352377084	0.00443325255733828
EGR1#1958	6	4.98817909481014	6.48943962979974e-05	0.00105519318931442
FOSL1#8061	2	13.2378599054577	0.0088883308800909	0.0337216066835881
HDAC2#3066	6	13.4156202366263	1.71355402088576e-07	9.4240057075981e-06
HMGN3#9324	4	5.45236514890039	0.00272961688233377	0.0149883521332312
IRF1#3659	4	5.09144250237593	0.00353524076589381	0.0179449336743224
JUND#3727	6	6.99466394187103	8.53468650061654e-06	0.000232183934211485
MAX#4149	4	4.30170367267141	0.00664492391067637	0.0282995232356208
NR3C1#2908	4	9.98201555411536	0.000267321918040192	0.00286053624981554
PAX5#5079	4	4.44637702078522	0.00587473351924079	0.0263643560508761
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380364143298006
RAD21#5885	4	6.90335593030422	0.0011108515162536	0.00771384451502727
REST#5978	4	6.43335247741868	0.00145495422303207	0.00932576188162799
SIN3A#25942	4	3.60592315121009	0.0127389384448714	0.045943849445539
SMC3#9126	4	10.0299552299552	0.000262388182106552	0.00281062147190012
SRF#6722	4	9.1981188414452	0.000367240458248586	0.00365835809033042
STAT1#6772	4	13.8043916647995	7.53702299850546e-05	0.00116650732800965
TAF7#6879	4	7.62204626994928	0.00075927901514148	0.00596721657478825
TCF12#6938	4	7.08964326812428	0.00100299157265771	0.00718804891626969
TCF7L2#6934	4	7.18011770875823	0.000955329712067973	0.00687667515326122
ZBTB7A#51341	4	4.90127287191726	0.00407962811884375	0.0194882807073102
ZNF143#7702	4	9.00058436815194	0.000399481819713381	0.00390066209508655

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.