Coexpression cluster:C1314

Full id: C1314_bile_lung_hepatoma_Hepatocyte_Mast_choriocarcinoma_giant

Phase1 CAGE Peaks

Hg19::chr10:5138470..5138477,+	p@chr10:5138470..5138477 +
Hg19::chr10:5138548..5138561,+	p@chr10:5138548..5138561 +
Hg19::chr2:209118767..209118804,-	p6@IDH1
Hg19::chr2:209118811..209118822,-	p12@IDH1
Hg19::chr2:209118837..209118850,-	p9@IDH1
Hg19::chr5:133945416..133945452,-	p@chr5:133945416..133945452 -

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
metabolising cell	2.14e-09	12
endopolyploid cell	2.14e-09	12
parenchymal cell	2.14e-09	12
polyploid cell	2.14e-09	12
hepatocyte	2.14e-09	12
epithelial cell	2.64e-07	253
endodermal cell	6.47e-07	58

Uber Anatomy

Ontology term	p-value	n
subdivision of digestive tract	6.00e-10	118
endoderm-derived structure	9.24e-10	160
endoderm	9.24e-10	160
presumptive endoderm	9.24e-10	160
digestive system	5.63e-09	145
digestive tract	5.63e-09	145
primitive gut	5.63e-09	145
larynx	1.52e-08	9
epithelium of foregut-midgut junction	3.34e-07	25
anatomical boundary	3.34e-07	25
hepatobiliary system	3.34e-07	25
foregut-midgut junction	3.34e-07	25
septum transversum	3.34e-07	25
hepatic diverticulum	3.96e-07	22
liver primordium	3.96e-07	22
liver	8.16e-07	19
digestive gland	8.16e-07	19
liver bud	8.16e-07	19

Disease

Ontology term	p-value	n
carcinoma	1.15e-13	106
cancer	5.98e-12	235
disease of cellular proliferation	2.19e-11	239
cell type cancer	2.64e-11	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
ESRRA#2101	3	241.920157068063	1.74384396582811e-07	9.57043194677468e-06
FOSL2#2355	3	8.46510030228085	0.00359831563461509	0.0182190568945346
FOXA1#3169	4	7.38761316625697	0.000856262554534609	0.00644566851182356
FOXA2#3170	4	16.4203091684435	3.8126130114368e-05	0.000719135796101585
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287438321058024
GTF2F1#2962	3	6.36983043837883	0.00806820819630316	0.0319119710590307
HNF4A#3172	3	11.5661451814768	0.00146348715008573	0.00937585170333725
HNF4G#3174	3	14.3767112632234	0.000776977293719738	0.00608935401311689
NANOG#79923	3	14.6223892405063	0.00073945629288338	0.00582545642094345
NR3C1#2908	3	7.48651166558652	0.0051086696598407	0.0237563716373883
RXRA#6256	3	10.0373085695666	0.00220541911678922	0.012704454889043
SMC3#9126	3	7.52246642246642	0.00503954071682855	0.0234788148692893
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0279978034278957
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472380124889559
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.0463981539821046
TFAP2A#7020	3	8.25931718652248	0.00386073847705559	0.0190427725420425
TFAP2C#7022	3	5.40461430493011	0.0127757616669587	0.0460591588503402
ZNF143#7702	3	6.75043827611395	0.00685025920446858	0.0290343014104742

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.