Coexpression cluster:C4117

Full id: C4117_Urothelial_small_Corneal_tubular_Smooth_cervical_pharyngeal

Phase1 CAGE Peaks

Hg19::chr2:110873370..110873379,-	p3@MALL
Hg19::chr2:110873388..110873405,-	p1@MALL
Hg19::chr2:110873422..110873434,-	p2@MALL

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><br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.55e-18	254
embryonic cell	3.04e-12	248
meso-epithelial cell	1.02e-11	44
endothelial cell	2.04e-11	35
endothelial cell of vascular tree	3.08e-11	24
blood vessel endothelial cell	6.43e-10	18
embryonic blood vessel endothelial progenitor cell	6.43e-10	18
mesodermal cell	9.91e-10	119
squamous epithelial cell	1.28e-09	62
endo-epithelial cell	4.98e-09	43
kidney cell	2.29e-08	18
kidney epithelial cell	2.29e-08	18
epithelial cell of nephron	7.66e-08	16
lining cell	2.82e-07	57
barrier cell	2.82e-07	57
endodermal cell	5.92e-07	59

Uber Anatomy

Ontology term	p-value	n
epithelium	7.09e-25	309
anatomical conduit	9.43e-25	241
cell layer	1.79e-24	312
anatomical system	2.27e-22	625
multi-cellular organism	2.81e-22	659
anatomical group	4.80e-22	626
anatomical cluster	1.11e-21	286
multi-tissue structure	1.02e-20	347
organism subdivision	1.57e-19	365
epithelial tube	8.92e-19	118
tube	2.57e-17	194
trunk	2.90e-15	216
endoderm-derived structure	9.07e-15	169
endoderm	9.07e-15	169
presumptive endoderm	9.07e-15	169
anatomical space	4.05e-14	104
mesenchyme	4.33e-14	238
entire embryonic mesenchyme	4.33e-14	238
organ part	4.55e-14	219
splanchnic layer of lateral plate mesoderm	6.31e-14	84
vessel	7.43e-14	69
embryonic structure	1.16e-13	605
developing anatomical structure	1.16e-13	605
embryo	1.74e-13	612
germ layer	2.49e-13	604
embryonic tissue	2.49e-13	604
presumptive structure	2.49e-13	604
epiblast (generic)	2.49e-13	604
vasculature	5.02e-13	79
vascular system	5.02e-13	79
blood vessel	1.07e-12	60
epithelial tube open at both ends	1.07e-12	60
blood vasculature	1.07e-12	60
vascular cord	1.07e-12	60
compound organ	1.51e-12	69
immaterial anatomical entity	5.04e-12	126
digestive system	7.71e-12	155
digestive tract	7.71e-12	155
primitive gut	7.71e-12	155
subdivision of digestive tract	1.40e-11	129
endodermal part of digestive tract	1.40e-11	129
simple squamous epithelium	1.42e-11	22
unilaminar epithelium	4.36e-11	138
renal system	6.37e-11	45
trunk region element	6.53e-11	107
organ	7.28e-11	511
urinary system structure	1.08e-10	44
squamous epithelium	1.61e-10	25
intermediate mesoderm	3.19e-10	37
endothelium	6.43e-10	18
blood vessel endothelium	6.43e-10	18
cardiovascular system endothelium	6.43e-10	18
subdivision of trunk	1.19e-09	113
epithelial fold	5.61e-09	51
circulatory system	9.14e-09	113
mixed endoderm/mesoderm-derived structure	1.01e-08	130
duct	1.19e-08	26
cardiovascular system	2.80e-08	110
anatomical cavity	2.86e-08	70
trunk mesenchyme	4.06e-08	143
body cavity precursor	4.83e-08	63
primordium	6.21e-08	168
nephron epithelium	7.66e-08	16
nephron	7.66e-08	16
uriniferous tubule	7.66e-08	16
metanephric mesenchyme	7.66e-08	16
nephrogenic mesenchyme	7.66e-08	16
excretory tube	9.09e-08	17
mesonephric epithelium	9.09e-08	17
mesonephric tubule	9.09e-08	17
nephric duct	9.09e-08	17
kidney epithelium	9.09e-08	17
renal duct	9.09e-08	17
mesonephric duct	9.09e-08	17
pronephric duct	9.09e-08	17
urogenital ridge	1.11e-07	20
thoracic segment of trunk	1.12e-07	52
artery	1.38e-07	42
arterial blood vessel	1.38e-07	42
arterial system	1.38e-07	42
mesonephros	1.44e-07	18
pronephros	1.44e-07	18
nephrogenic cord	1.44e-07	18

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280021133119857
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326060606132738
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.00067795727235294
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295070382698489

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.