Coexpression cluster:C1607

Full id: C1607_seminal_ductus_Hepatocyte_epididymis_pancreas_kidney_stomach

Phase1 CAGE Peaks

Hg19::chr11:111170526..111170544,-	p3@C11orf92
Hg19::chr11:111852954..111852989,+	p7@DIXDC1
Hg19::chr12:18414395..18414406,+	p3@PIK3C2G
Hg19::chr19:14172840..14172853,-	p@chr19:14172840..14172853 -
Hg19::chr19:14172854..14172901,-	p@chr19:14172854..14172901 -

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:0035005	phosphatidylinositol-4-phosphate 3-kinase activity	0.0105966502627415
GO:0035004	phosphoinositide 3-kinase activity	0.0131152207783198
GO:0016303	1-phosphatidylinositol-3-kinase activity	0.0131152207783198
GO:0005942	phosphoinositide 3-kinase complex	0.0131152207783198
GO:0016307	phosphatidylinositol phosphate kinase activity	0.0131152207783198
GO:0046854	phosphoinositide phosphorylation	0.0131152207783198
GO:0046834	lipid phosphorylation	0.0131152207783198
GO:0001727	lipid kinase activity	0.0167693862056444
GO:0030258	lipid modification	0.020393644455001
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0232910130371656
GO:0030384	phosphoinositide metabolic process	0.0256597345886452
GO:0006650	glycerophospholipid metabolic process	0.0296866077337913
GO:0048015	phosphoinositide-mediated signaling	0.0349854547671642
GO:0016055	Wnt receptor signaling pathway	0.0365072107407221
GO:0044445	cytosolic part	0.044618264677261
GO:0006644	phospholipid metabolic process	0.0473160554453427

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
chorionic membrane mesenchymal stem cell	7.97e-09	3
endodermal cell	4.26e-07	58

Uber Anatomy

Ontology term	p-value	n
subdivision of digestive tract	2.20e-13	118
digestive system	3.80e-13	145
digestive tract	3.80e-13	145
primitive gut	3.80e-13	145
trunk region element	1.72e-12	101
endoderm-derived structure	6.10e-12	160
endoderm	6.10e-12	160
presumptive endoderm	6.10e-12	160
immaterial anatomical entity	8.11e-11	117
adult organism	1.23e-10	114
male genital duct	1.02e-09	3
internal male genitalia	1.02e-09	3
acellular anatomical structure	7.97e-09	3
egg chorion	7.97e-09	3
subdivision of trunk	1.54e-08	112
endo-epithelium	2.29e-08	82
abdomen element	2.54e-08	54
abdominal segment element	2.54e-08	54
anatomical space	1.25e-07	95
foregut	1.44e-07	87
duct of male reproductive system	2.38e-07	4
abdominal segment of trunk	4.03e-07	60
abdomen	4.03e-07	60
gut epithelium	4.29e-07	54
internal genitalia	5.97e-07	25
major salivary gland	7.43e-07	2

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
GATA3#2625	2	10.8946065428824	0.012515829121883	0.0452767813529735

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.