Coexpression cluster:C3652

Full id: C3652_Bronchial_meningioma_papillary_Prostate_mesenchymal_Tracheal_Urothelial

Phase1 CAGE Peaks

Hg19::chr17:48141446..48141483,+	p@chr17:48141446..48141483 +
Hg19::chr17:48145468..48145508,+	p@chr17:48145468..48145508 +
Hg19::chr17:48149430..48149463,+	p5@ITGA3

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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No GOStat results

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	2.14e-31	254
embryonic cell	5.17e-26	248
endo-epithelial cell	2.84e-13	43
non-terminally differentiated cell	2.45e-10	180
kidney cell	1.23e-09	18
kidney epithelial cell	1.23e-09	18
animal cell	1.25e-09	679
eukaryotic cell	1.25e-09	679
epithelial cell of nephron	1.32e-09	16
mesodermal cell	2.67e-09	119
mesothelial cell	2.98e-09	19
squamous epithelial cell	5.78e-09	62
endodermal cell	6.07e-09	59
ecto-epithelial cell	1.40e-08	33
ectodermal cell	6.98e-08	71
kidney cortical cell	7.50e-08	13
renal cortical epithelial cell	7.50e-08	13
respiratory epithelial cell	8.72e-08	13
kidney tubule cell	1.04e-07	12
nephron tubule epithelial cell	1.04e-07	12
columnar/cuboidal epithelial cell	7.21e-07	27

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	1.86e-14	347
mesenchyme	4.39e-13	238
entire embryonic mesenchyme	4.39e-13	238
trunk mesenchyme	4.71e-12	143
organism subdivision	3.52e-11	365
trunk	1.01e-10	216
cell layer	4.67e-10	312
duct	7.52e-10	26
epithelium	7.70e-10	309
nephron epithelium	1.32e-09	16
nephron	1.32e-09	16
uriniferous tubule	1.32e-09	16
metanephric mesenchyme	1.32e-09	16
nephrogenic mesenchyme	1.32e-09	16
urogenital ridge	1.86e-09	20
excretory tube	4.16e-09	17
mesonephric epithelium	4.16e-09	17
mesonephric tubule	4.16e-09	17
nephric duct	4.16e-09	17
kidney epithelium	4.16e-09	17
renal duct	4.16e-09	17
mesonephric duct	4.16e-09	17
pronephric duct	4.16e-09	17
mesonephros	5.87e-09	18
pronephros	5.87e-09	18
nephrogenic cord	5.87e-09	18
pronephric mesoderm	5.87e-09	18
rostral part of nephrogenic cord	5.87e-09	18
presumptive pronephric mesoderm	5.87e-09	18
multilaminar epithelium	8.51e-09	82
epithelial tube	6.65e-08	118
cortex of kidney	7.50e-08	13
renal parenchyma	7.50e-08	13
parenchyma	8.35e-08	17
renal tubule	1.04e-07	12
nephron tubule	1.04e-07	12
nephron tubule epithelium	1.04e-07	12
somite	1.27e-07	83
paraxial mesoderm	1.27e-07	83
presomitic mesoderm	1.27e-07	83
presumptive segmental plate	1.27e-07	83
trunk paraxial mesoderm	1.27e-07	83
presumptive paraxial mesoderm	1.27e-07	83
anatomical system	1.44e-07	625
multi-cellular organism	1.64e-07	659
urinary system structure	1.93e-07	44
intermediate mesoderm	2.01e-07	37
anatomical group	2.17e-07	626
primordium	2.49e-07	168
intraembryonic coelom	2.58e-07	21
anatomical space	3.17e-07	104
renal system	6.23e-07	45
ectodermal placode	7.25e-07	29
dermomyotome	7.44e-07	70

Disease

Ontology term	p-value	n
reproductive organ cancer	4.45e-08	29
female reproductive organ cancer	5.67e-08	27

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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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.