Coexpression cluster:C1004

Full id: C1004_chorionic_pancreatic_choriocarcinoma_amniotic_placenta_colon_Placental

Phase1 CAGE Peaks

Hg19::chr11:7595176..7595189,+	p19@PPFIBP2
Hg19::chr17:73982309..73982324,+	p4@TEN1
Hg19::chr20:18125679..18125686,+	p7@CSRP2BP
Hg19::chr20:18125727..18125755,+	p4@CSRP2BP
Hg19::chr20:18125925..18125964,+	p5@CSRP2BP
Hg19::chrX:52112136..52112150,+	p3@XAGE2B p3@XAGE2
Hg19::chrX:52112158..52112165,+	p1@XAGE2B p1@XAGE2
Hg19::chrX:52386980..52387013,-	p2@XAGE2B p2@XAGE2

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:0030274	LIM domain binding	0.0105961823506016
GO:0008907	integrase activity	0.0150088277864031
GO:0015074	DNA integration	0.0182422653092127
GO:0008080	N-acetyltransferase activity	0.0261641131540075
GO:0016407	acetyltransferase activity	0.0261641131540075
GO:0016410	N-acyltransferase activity	0.0261641131540075
GO:0019904	protein domain specific binding	0.0319837703946395
GO:0008415	acyltransferase activity	0.049075006499733
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.049075006499733

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
extraembryonic cell	3.65e-41	19
chorionic membrane mesenchymal stem cell	9.13e-22	3
placental epithelial cell	1.07e-20	3
germ line cell	6.46e-16	7
germ cell	6.46e-16	7
amniotic epithelial cell	3.31e-14	2
amnion mesenchymal stem cell	7.38e-13	5
serous secreting cell	8.69e-08	1
intestinal epithelial cell	1.35e-07	4

Uber Anatomy

Ontology term	p-value	n
extraembryonic membrane	1.65e-67	14
membranous layer	1.65e-67	14
chorion	3.12e-47	7
extraembryonic structure	1.77e-38	24
placenta	2.89e-27	4
allantois	2.89e-27	4
amnion	7.04e-24	7
acellular anatomical structure	9.13e-22	3
egg chorion	9.13e-22	3
somatic layer of lateral plate mesoderm	6.99e-21	8
organ component layer	5.40e-20	66
uterus	6.53e-11	21
embryonic uterus	2.16e-10	22
internal female genitalia	2.16e-10	22
internal genitalia	4.41e-09	25
female reproductive organ	5.97e-08	37
female reproductive system	5.97e-08	37
epithelium of female gonad	8.69e-08	1
rectum	1.10e-07	4
reproductive organ	1.14e-07	48
reproductive structure	1.17e-07	59
reproductive system	1.17e-07	59
intestinal mucosa	1.35e-07	4
wall of intestine	1.35e-07	4
gastrointestinal system mucosa	1.35e-07	4
gastrointestinal system epithelium	1.35e-07	4
intestinal epithelium	1.35e-07	4
female organism	4.28e-07	41

Disease

Ontology term	p-value	n
islet cell tumor	2.04e-08	1
endocrine pancreas cancer	2.04e-08	1
pancreatic endocrine carcinoma	2.04e-08	1
ovary epithelial cancer	8.69e-08	1

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)
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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
BHLHE40#8553	2	11.2179533867444	0.012714725561129	0.0458676115809038
HNF4A#3172	3	8.67460888610763	0.00383847087411728	0.0189392006246485
HNF4G#3174	3	10.7825334474175	0.00206426737520625	0.0119712377366409

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.