Coexpression cluster:C4826

Full id: C4826_hepatocellular_Renal_kidney_adenocarcinoma_Intestinal_small_Prostate

Phase1 CAGE Peaks

Hg19::chr9:71735882..71735896,+	p6@TJP2
Hg19::chr9:71735910..71735923,+	p16@TJP2
Hg19::chr9:71735943..71735948,+	p26@TJP2

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	3.31e-19	254
kidney tubule cell	8.36e-15	12
nephron tubule epithelial cell	8.36e-15	12
epithelial cell of nephron	3.61e-14	16
kidney cell	3.94e-12	18
kidney epithelial cell	3.94e-12	18
kidney cortical cell	2.77e-10	13
renal cortical epithelial cell	2.77e-10	13
germ line cell	2.31e-07	7
germ cell	2.31e-07	7
embryonic stem cell	4.79e-07	5

Uber Anatomy

Ontology term	p-value	n
excretory tube	6.11e-15	17
mesonephric epithelium	6.11e-15	17
mesonephric tubule	6.11e-15	17
nephric duct	6.11e-15	17
kidney epithelium	6.11e-15	17
renal duct	6.11e-15	17
mesonephric duct	6.11e-15	17
pronephric duct	6.11e-15	17
renal tubule	8.36e-15	12
nephron tubule	8.36e-15	12
nephron tubule epithelium	8.36e-15	12
immaterial anatomical entity	1.03e-14	126
nephron epithelium	3.61e-14	16
nephron	3.61e-14	16
uriniferous tubule	3.61e-14	16
metanephric mesenchyme	3.61e-14	16
nephrogenic mesenchyme	3.61e-14	16
duct	5.04e-14	26
urogenital ridge	7.15e-14	20
mesonephros	7.39e-14	18
pronephros	7.39e-14	18
nephrogenic cord	7.39e-14	18
pronephric mesoderm	7.39e-14	18
rostral part of nephrogenic cord	7.39e-14	18
presumptive pronephric mesoderm	7.39e-14	18
intermediate mesoderm	1.95e-13	37
intraembryonic coelom	9.74e-13	21
urinary system structure	1.04e-12	44
renal system	2.94e-12	45
kidney	4.41e-12	27
kidney mesenchyme	4.41e-12	27
kidney rudiment	4.41e-12	27
kidney field	4.41e-12	27
body cavity precursor	4.73e-12	63
cavitated compound organ	4.96e-12	32
anatomical space	6.28e-12	104
anatomical cavity	1.05e-11	70
subdivision of digestive tract	1.17e-11	129
endodermal part of digestive tract	1.17e-11	129
abdomen element	5.55e-11	55
abdominal segment element	5.55e-11	55
trunk region element	8.99e-11	107
digestive system	2.54e-10	155
digestive tract	2.54e-10	155
primitive gut	2.54e-10	155
cortex of kidney	2.77e-10	13
renal parenchyma	2.77e-10	13
male organism	1.44e-09	22
male reproductive system	1.44e-09	22
male reproductive organ	1.99e-09	11
endoderm-derived structure	2.62e-09	169
endoderm	2.62e-09	169
presumptive endoderm	2.62e-09	169
abdominal segment of trunk	3.85e-09	61
abdomen	3.85e-09	61
gastrointestinal system	9.37e-09	35
intestine	1.45e-08	27
anatomical conduit	6.97e-08	241
cortex	7.75e-08	16
mixed endoderm/mesoderm-derived structure	8.79e-08	130
subdivision of trunk	1.21e-07	113
reproductive structure	2.54e-07	59
reproductive system	2.54e-07	59
parenchyma	3.21e-07	17
hindgut	5.40e-07	19

Disease

Ontology term	p-value	n
carcinoma	1.10e-15	106
cell type cancer	3.17e-11	143
adenocarcinoma	1.41e-08	25

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
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.00077982448884291
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0328252915557331
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465411818644468
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256571768528926
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168658525376677
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00902660274004865
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00244223909955949
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000856000121670352
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00394038250423405
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123579977530795
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157824967374295
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296490194899416
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000742118493282762
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310650086528226
POU5F1#5460	3	335.439201451906	2.63510205045339e-08	1.82498291145426e-06
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00166141145545717
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278622844726613
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248179262391327
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00546298605170008
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00632563115264981
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191378238060808
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331597079190248
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110277232387706

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.