Coexpression cluster:C611

Full id: C611_small_hepatocellular_colon_adenocarcinoma_Intestinal_signet_temporal

Phase1 CAGE Peaks

Hg19::chr10:102729876..102729890,-	p1@AK000735
Hg19::chr10:102729908..102729938,-	p2@AK000735
Hg19::chr13:76335013..76335032,+	p14@LMO7
Hg19::chr16:2034715..2034726,+	p10@GFER
Hg19::chr16:75284758..75284802,-	p@chr16:75284758..75284802 -
Hg19::chr2:233742013..233742020,-	p@chr2:233742013..233742020 -
Hg19::chr2:61245275..61245310,-	p6@PUS10
Hg19::chr2:74753294..74753302,-	p6@DQX1
Hg19::chr2:74753305..74753331,-	p2@DQX1
Hg19::chr2:74753332..74753373,-	p1@DQX1
Hg19::chr3:8693755..8693789,-	p1@C3orf32
Hg19::chr6:158993336..158993351,+	p10@TMEM181
Hg19::chr7:55256663..55256679,-	p2@ENST00000442411 p2@uc003tqo.2
Hg19::chr9:86571432..86571453,-	p5@C9orf64

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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GO ID	GO name	FDR corrected p-value
GO:0016972	thiol oxidase activity	0.0141274113637933
GO:0016670	oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor	0.0141274113637933

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><br>

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Cell Type

Ontology term	p-value	n
intestinal epithelial cell	2.36e-09	4
metabolising cell	4.59e-07	12
endopolyploid cell	4.59e-07	12
parenchymal cell	4.59e-07	12
polyploid cell	4.59e-07	12
hepatocyte	4.59e-07	12

Uber Anatomy

Ontology term	p-value	n
intestine	9.34e-37	17
gastrointestinal system	7.88e-31	25
colon	3.27e-23	9
large intestine	5.57e-19	11
small intestine	4.04e-16	4
subdivision of digestive tract	2.65e-13	118
digestive system	5.89e-12	145
digestive tract	5.89e-12	145
primitive gut	5.89e-12	145
endoderm-derived structure	1.41e-10	160
endoderm	1.41e-10	160
presumptive endoderm	1.41e-10	160
vermiform appendix	1.48e-09	1
caecum	1.48e-09	1
midgut	1.48e-09	1
intestinal mucosa	2.36e-09	4
wall of intestine	2.36e-09	4
gastrointestinal system mucosa	2.36e-09	4
gastrointestinal system epithelium	2.36e-09	4
intestinal epithelium	2.36e-09	4
nucleus accumbens	2.67e-09	1
ventral striatum	2.67e-09	1
digestive tract diverticulum	4.59e-09	23
gut epithelium	6.13e-09	54
epithelium of foregut-midgut junction	2.41e-08	25
anatomical boundary	2.41e-08	25
hepatobiliary system	2.41e-08	25
foregut-midgut junction	2.41e-08	25
septum transversum	2.41e-08	25
sac	5.37e-08	26
organ system subdivision	1.05e-07	223
lower digestive tract	1.66e-07	5
liver	2.26e-07	19
digestive gland	2.26e-07	19
liver bud	2.26e-07	19

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	6	3.41620612535349	0.00475176856810538	0.0223343815249486
ELF1#1997	9	2.73734868780485	0.00133657072811265	0.00886962195154133
EP300#2033	8	3.87082384355611	0.000292351760388241	0.00310262427631212
FOSL2#2355	4	4.83720017273191	0.00754162287399241	0.0310877625251379
FOXA1#3169	9	7.12376983889065	5.19704363903544e-07	2.42743309757255e-05
FOXA2#3170	7	12.3152318763326	4.83510549852797e-07	2.27876165686265e-05
HDAC2#3066	8	7.66606870664358	1.89551452608875e-06	6.97799230138115e-05
HEY1#23462	14	4.04011104310571	3.23477172841824e-09	2.67487192829986e-07
HNF4A#3172	12	19.8276774539603	3.54543106940285e-15	6.31879309654204e-13
HNF4G#3174	9	18.4843430527158	1.26472046417331e-10	1.35612053960777e-08
NR2C2#7182	4	9.31846025864025	0.000690363193353926	0.00556548371676501
POLR2A#5430	14	2.14745317655807	2.25331953374171e-05	0.000492434481658192
RXRA#6256	9	12.9051110180142	2.9964879042402e-09	2.51163884615523e-07
SIN3A#25942	9	3.47714018152402	0.000204086532801336	0.00242211288627713
SP1#6667	9	3.66324517166201	0.000134181452530633	0.00175941955063989
SRF#6722	5	4.92756366505993	0.00229448556458705	0.0130179149217681
TAF1#6872	10	2.38789020410378	0.0016242233760895	0.010167971298652
TBP#6908	9	2.38292401313339	0.00381176112623516	0.0188243105855341
TCF7L2#6934	7	5.38508828156867	0.000113022621779428	0.00154887411048703

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.