Coexpression cluster:C1294

Full id: C1294_Hepatocyte_kidney_liver_seminal_salivary_ductus_thyroid

Phase1 CAGE Peaks

Hg19::chr10:104597286..104597295,-	p5@CYP17A1
Hg19::chr10:104597311..104597320,-	p4@CYP17A1
Hg19::chr10:104597342..104597349,-	p6@CYP17A1
Hg19::chr16:20548438..20548449,-	p2@ACSM2B
Hg19::chr16:20548514..20548523,-	p3@ACSM2B
Hg19::chr18:42277095..42277130,+	p8@SETBP1

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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p.value	FDR	nGenes	nPathway	Name
6.15571812123322e-05	0.0389656957074063	2	130	Biological oxidations (Reactome):REACT_13433

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:0004508	steroid 17-alpha-monooxygenase activity	0.00732956552454962
GO:0006704	glucocorticoid biosynthetic process	0.0122145041866808
GO:0047760	butyrate-CoA ligase activity	0.0122145041866808
GO:0008211	glucocorticoid metabolic process	0.0128244743045017
GO:0006700	C21-steroid hormone biosynthetic process	0.0154653297256805
GO:0008395	steroid hydroxylase activity	0.0154653297256805
GO:0008207	C21-steroid hormone metabolic process	0.0154653297256805
GO:0044255	cellular lipid metabolic process	0.0154653297256805
GO:0016878	acid-thiol ligase activity	0.0154653297256805
GO:0009636	response to toxin	0.0162555467239316
GO:0006629	lipid metabolic process	0.0162555467239316
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.0162555467239316
GO:0005739	mitochondrion	0.0162555467239316
GO:0030424	axon	0.0170852081807174
GO:0043025	cell soma	0.0170852081807174
GO:0042446	hormone biosynthetic process	0.0196738632930984
GO:0019825	oxygen binding	0.0245351119003364
GO:0043005	neuron projection	0.0295746793628032
GO:0007548	sex differentiation	0.0295746793628032
GO:0003006	reproductive developmental process	0.0295746793628032
GO:0042445	hormone metabolic process	0.0295746793628032
GO:0006694	steroid biosynthetic process	0.0295746793628032
GO:0005792	microsome	0.0485203145647627
GO:0042598	vesicular fraction	0.0485203145647627
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0485203145647627
GO:0031980	mitochondrial lumen	0.0485203145647627
GO:0005759	mitochondrial matrix	0.0485203145647627
GO:0006631	fatty acid metabolic process	0.0485203145647627
GO:0043231	intracellular membrane-bound organelle	0.0485203145647627
GO:0043227	membrane-bound organelle	0.0485203145647627

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
metabolising cell	3.56e-19	12
endopolyploid cell	3.56e-19	12
parenchymal cell	3.56e-19	12
polyploid cell	3.56e-19	12
hepatocyte	3.56e-19	12

Uber Anatomy

Ontology term	p-value	n
endocrine gland	2.50e-19	35
liver	1.23e-18	19
digestive gland	1.23e-18	19
liver bud	1.23e-18	19
hepatic diverticulum	4.17e-16	22
liver primordium	4.17e-16	22
digestive tract diverticulum	2.08e-15	23
endocrine system	6.16e-15	45
epithelial sac	3.53e-14	25
epithelium of foregut-midgut junction	3.53e-14	25
anatomical boundary	3.53e-14	25
hepatobiliary system	3.53e-14	25
foregut-midgut junction	3.53e-14	25
septum transversum	3.53e-14	25
sac	1.23e-13	26
abdomen element	2.04e-12	54
abdominal segment element	2.04e-12	54
gut epithelium	2.28e-12	54
thyroid gland	2.52e-12	5
pharyngeal pouch	2.52e-12	5
thyroid diverticulum	2.52e-12	5
pharyngeal pouch 2	2.52e-12	5
thyroid primordium	2.52e-12	5
exocrine gland	1.95e-11	31
exocrine system	1.95e-11	31
gland	2.80e-11	59
abdominal segment of trunk	4.00e-11	60
abdomen	4.00e-11	60
endo-epithelium	2.45e-10	82
trunk region element	2.80e-08	101
subdivision of trunk	2.17e-07	112

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.