Coexpression cluster:C2478

Full id: C2478_testicular_chorionic_placenta_anaplastic_amniotic_choriocarcinoma_Placental

Phase1 CAGE Peaks

Hg19::chr19:1584937..1584949,-	p1@M77818
Hg19::chr19:1584956..1584968,-	p2@M77818
Hg19::chr3:49506374..49506387,+	p15@DAG1
Hg19::chr7:97984753..97984783,-	p9@BAIAP2L1

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:0002011	morphogenesis of an epithelial sheet	0.00423872249338194
GO:0005055	laminin receptor activity	0.00423872249338194
GO:0016011	dystroglycan complex	0.0112995998696127
GO:0042383	sarcolemma	0.0112995998696127
GO:0009653	anatomical structure morphogenesis	0.0112995998696127
GO:0005626	insoluble fraction	0.0112995998696127
GO:0016010	dystrophin-associated glycoprotein complex	0.0112995998696127
GO:0046847	filopodium formation	0.0112995998696127
GO:0030035	microspike biogenesis	0.0112995998696127
GO:0005605	basal lamina	0.0169454069541581
GO:0045121	lipid raft	0.0176488660653594
GO:0030031	cell projection biogenesis	0.0176488660653594
GO:0048856	anatomical structure development	0.0190571256358965
GO:0002009	morphogenesis of an epithelium	0.0190571256358965
GO:0005604	basement membrane	0.0208888706484029
GO:0044420	extracellular matrix part	0.0346386466874561
GO:0016043	cellular component organization and biogenesis	0.0349345137723753
GO:0003012	muscle system process	0.0349345137723753
GO:0006936	muscle contraction	0.0349345137723753
GO:0032502	developmental process	0.0349345137723753
GO:0032990	cell part morphogenesis	0.0374838474864422
GO:0030030	cell projection organization and biogenesis	0.0374838474864422
GO:0048858	cell projection morphogenesis	0.0374838474864422
GO:0032501	multicellular organismal process	0.0379629128886618
GO:0015629	actin cytoskeleton	0.0499693031959513

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	3.49e-16	254
endodermal cell	1.95e-13	59
endo-epithelial cell	9.34e-12	43
germ line cell	8.62e-11	7
germ cell	8.62e-11	7

Uber Anatomy

Ontology term	p-value	n
extraembryonic membrane	1.59e-13	14
membranous layer	1.59e-13	14
reproductive structure	1.86e-09	59
reproductive system	1.86e-09	59
endoderm-derived structure	2.44e-08	169
endoderm	2.44e-08	169
presumptive endoderm	2.44e-08	169
chorion	5.34e-08	7
reproductive organ	1.19e-07	48
subdivision of digestive tract	1.34e-07	129
endodermal part of digestive tract	1.34e-07	129
mixed endoderm/mesoderm-derived structure	2.11e-07	130
amnion	3.74e-07	7
male organism	5.08e-07	22
male reproductive system	5.08e-07	22
digestive system	6.34e-07	155
digestive tract	6.34e-07	155
primitive gut	6.34e-07	155

Disease

Ontology term	p-value	n
cell type cancer	5.88e-25	143
carcinoma	2.54e-22	106
cancer	5.74e-17	235
disease of cellular proliferation	4.31e-16	239
adenocarcinoma	3.02e-08	25

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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No analysis results for this cluster

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.