Coexpression cluster:C2891

Full id: C2891_Mesenchymal_uterus_smallcell_small_leiomyoma_cervix_acute

Phase1 CAGE Peaks

Hg19::chr7:27224795..27224840,-	p2@HOXA11
Hg19::chr7:27224842..27224872,-	p1@HOXA11
Hg19::chr7:27225007..27225030,+	p2@HOXA11-AS1
Hg19::chr7:27225038..27225057,+	p1@HOXA11-AS1

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:0001759	induction of an organ	0.00323796067349582
GO:0010092	specification of organ identity	0.00323796067349582
GO:0045168	cell-cell signaling during cell fate commitment	0.00323796067349582
GO:0031128	induction	0.00323796067349582
GO:0001656	metanephros development	0.00777110561638996
GO:0001822	kidney development	0.00925131620998805
GO:0001655	urogenital system development	0.00925131620998805
GO:0045165	cell fate commitment	0.0143684504886377
GO:0003002	regionalization	0.0156501432552298
GO:0007389	pattern specification process	0.0200753561756741
GO:0001501	skeletal development	0.0307606263982103
GO:0009887	organ morphogenesis	0.048839240158562

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 cell	4.17e-08	18
kidney epithelial cell	4.17e-08	18
epithelial cell of nephron	2.10e-07	16
skin fibroblast	2.63e-07	23
kidney tubule cell	4.64e-07	12
nephron tubule epithelial cell	4.64e-07	12

Uber Anatomy

Ontology term	p-value	n
renal system	5.37e-19	45
urinary system structure	1.64e-18	44
intermediate mesoderm	1.63e-12	37
cavitated compound organ	1.97e-10	32
kidney	2.72e-10	27
kidney mesenchyme	2.72e-10	27
kidney rudiment	2.72e-10	27
kidney field	2.72e-10	27
mesonephros	1.57e-08	18
pronephros	1.57e-08	18
nephrogenic cord	1.57e-08	18
pronephric mesoderm	1.57e-08	18
rostral part of nephrogenic cord	1.57e-08	18
presumptive pronephric mesoderm	1.57e-08	18
reproductive structure	1.84e-08	59
reproductive system	1.84e-08	59
urogenital ridge	2.77e-08	20
cloaca	4.67e-08	14
anal region	4.67e-08	14
embryonic cloaca	4.67e-08	14
terminal part of digestive tract	4.67e-08	14
primitive urogenital sinus	4.67e-08	14
proctodeum	4.67e-08	14
excretory tube	5.46e-08	17
mesonephric epithelium	5.46e-08	17
mesonephric tubule	5.46e-08	17
nephric duct	5.46e-08	17
kidney epithelium	5.46e-08	17
renal duct	5.46e-08	17
mesonephric duct	5.46e-08	17
pronephric duct	5.46e-08	17
hindgut	1.36e-07	19
nephron epithelium	2.10e-07	16
nephron	2.10e-07	16
uriniferous tubule	2.10e-07	16
metanephric mesenchyme	2.10e-07	16
nephrogenic mesenchyme	2.10e-07	16
male organism	2.60e-07	22
male reproductive system	2.60e-07	22
genitourinary system	3.60e-07	15
renal tubule	4.64e-07	12
nephron tubule	4.64e-07	12
nephron tubule epithelium	4.64e-07	12
sex gland	8.54e-07	12
male reproductive gland	8.54e-07	12

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.