Coexpression cluster:C1917

Full id: C1917_clear_epididymis_serous_uterus_kidney_B_ductus

Phase1 CAGE Peaks

Hg19::chr3:112127710..112127713,-	p@chr3:112127710..112127713 -
Hg19::chr3:112128019..112128034,-	p1@ENST00000486726
Hg19::chr3:112128117..112128134,-	p2@ENST00000486726
Hg19::chr5:138905822..138905827,+	p10@UBE2D2
Hg19::chr7:76911466..76911478,+	p4@CCDC146

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:0004842	ubiquitin-protein ligase activity	0.033249604249251
GO:0008639	small protein conjugating enzyme activity	0.033249604249251
GO:0019787	small conjugating protein ligase activity	0.033249604249251
GO:0006511	ubiquitin-dependent protein catabolic process	0.033249604249251
GO:0043632	modification-dependent macromolecule catabolic process	0.033249604249251
GO:0019941	modification-dependent protein catabolic process	0.033249604249251
GO:0051603	proteolysis involved in cellular protein catabolic process	0.033249604249251
GO:0044257	cellular protein catabolic process	0.033249604249251
GO:0016881	acid-amino acid ligase activity	0.033249604249251
GO:0030163	protein catabolic process	0.0337550710210548
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0337550710210548
GO:0051246	regulation of protein metabolic process	0.0349518608084486
GO:0043285	biopolymer catabolic process	0.0349518608084486
GO:0044265	cellular macromolecule catabolic process	0.0366301660190745
GO:0006512	ubiquitin cycle	0.0366301660190745
GO:0009057	macromolecule catabolic process	0.0380901919227599
GO:0016874	ligase activity	0.0380901919227599
GO:0044248	cellular catabolic process	0.0449814880228161

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
kidney tubule cell	8.72e-13	12
nephron tubule epithelial cell	8.72e-13	12
kidney cell	6.16e-12	18
kidney epithelial cell	6.16e-12	18
epithelial cell of nephron	4.71e-09	16
brush border epithelial cell	3.90e-07	3
kidney cortex tubule cell	3.90e-07	3
epithelial cell of proximal tubule	3.90e-07	3
kidney cortical cell	7.12e-07	13
renal cortical epithelial cell	7.12e-07	13

Uber Anatomy

Ontology term	p-value	n
urinary system structure	2.42e-18	44
cavitated compound organ	7.60e-18	32
renal system	8.88e-18	45
kidney	5.57e-16	27
kidney mesenchyme	5.57e-16	27
kidney rudiment	5.57e-16	27
kidney field	5.57e-16	27
abdomen element	3.08e-13	55
abdominal segment element	3.08e-13	55
renal tubule	8.72e-13	12
nephron tubule	8.72e-13	12
nephron tubule epithelium	8.72e-13	12
mesonephros	5.63e-12	18
pronephros	5.63e-12	18
nephrogenic cord	5.63e-12	18
pronephric mesoderm	5.63e-12	18
rostral part of nephrogenic cord	5.63e-12	18
presumptive pronephric mesoderm	5.63e-12	18
intraembryonic coelom	7.47e-12	21
abdominal segment of trunk	2.74e-11	61
abdomen	2.74e-11	61
excretory tube	1.44e-10	17
mesonephric epithelium	1.44e-10	17
mesonephric tubule	1.44e-10	17
nephric duct	1.44e-10	17
kidney epithelium	1.44e-10	17
renal duct	1.44e-10	17
mesonephric duct	1.44e-10	17
pronephric duct	1.44e-10	17
urogenital ridge	1.72e-10	20
duct	1.83e-10	26
male reproductive organ	2.25e-10	11
reproductive structure	3.46e-09	59
reproductive system	3.46e-09	59
nephron epithelium	4.71e-09	16
nephron	4.71e-09	16
uriniferous tubule	4.71e-09	16
metanephric mesenchyme	4.71e-09	16
nephrogenic mesenchyme	4.71e-09	16
adult organism	6.52e-09	115
reproductive organ	9.85e-09	48
intermediate mesoderm	1.15e-08	37
male organism	1.42e-08	22
male reproductive system	1.42e-08	22
body cavity precursor	2.85e-08	63
trunk region element	4.71e-08	107
testis	5.25e-08	8
internal genitalia	1.78e-07	25
male genital duct	2.31e-07	3
internal male genitalia	2.31e-07	3
renal cortex tubule	3.90e-07	3
region of nephron tubule	3.90e-07	3
proximal tubule	3.90e-07	3
anatomical cavity	6.44e-07	70
cortex of kidney	7.12e-07	13
renal parenchyma	7.12e-07	13

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.