Coexpression cluster:C1885

Full id: C1885_neuroectodermal_nonsmall_small_neuroblastoma_embryonic_merkel_hairy

Phase1 CAGE Peaks

Hg19::chr2:176971685..176971700,+	p6@HOXD11
Hg19::chr2:176971980..176971995,+	p9@HOXD11
Hg19::chr2:176972000..176972025,+	p4@HOXD11
Hg19::chr2:176972047..176972063,+	p7@HOXD11
Hg19::chr2:176972082..176972096,+	p8@HOXD11

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
kidney cell	6.64e-13	18
kidney epithelial cell	6.64e-13	18
kidney tubule cell	2.55e-11	12
nephron tubule epithelial cell	2.55e-11	12
epithelial cell of nephron	3.07e-11	16
kidney cortical cell	3.36e-08	13
renal cortical epithelial cell	3.36e-08	13
epithelial cell	9.80e-07	254

Uber Anatomy

Ontology term	p-value	n
urinary system structure	1.73e-15	44
renal system	6.39e-15	45
cavitated compound organ	1.40e-14	32
kidney	6.66e-14	27
kidney mesenchyme	6.66e-14	27
kidney rudiment	6.66e-14	27
kidney field	6.66e-14	27
urogenital ridge	1.74e-12	20
excretory tube	1.07e-11	17
mesonephric epithelium	1.07e-11	17
mesonephric tubule	1.07e-11	17
nephric duct	1.07e-11	17
kidney epithelium	1.07e-11	17
renal duct	1.07e-11	17
mesonephric duct	1.07e-11	17
pronephric duct	1.07e-11	17
renal tubule	2.55e-11	12
nephron tubule	2.55e-11	12
nephron tubule epithelium	2.55e-11	12
nephron epithelium	3.07e-11	16
nephron	3.07e-11	16
uriniferous tubule	3.07e-11	16
metanephric mesenchyme	3.07e-11	16
nephrogenic mesenchyme	3.07e-11	16
mesonephros	8.61e-11	18
pronephros	8.61e-11	18
nephrogenic cord	8.61e-11	18
pronephric mesoderm	8.61e-11	18
rostral part of nephrogenic cord	8.61e-11	18
presumptive pronephric mesoderm	8.61e-11	18
intermediate mesoderm	4.84e-10	37
larynx	1.68e-09	9
intraembryonic coelom	1.30e-08	21
cortex of kidney	3.36e-08	13
renal parenchyma	3.36e-08	13
duct	3.07e-07	26

Disease

Ontology term	p-value	n
cell type cancer	7.15e-15	143
disease of cellular proliferation	9.20e-11	239
carcinoma	3.54e-10	106
cancer	8.70e-10	235
neuroectodermal tumor	1.13e-07	10

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
ATF3#467	4	17.970539620807	1.89252338486495e-05	0.000429028108947059
CEBPB#1051	4	6.37691810065985	0.00111394417667732	0.0076569182485193
CTCF#10664	5	5.36025637307503	0.000225927829993709	0.00249980682664614
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00353172130793459
SUZ12#23512	5	50.1157809110629	3.15480790456198e-09	2.62537834856214e-07
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147218485056134
USF2#7392	4	10.3937579080557	0.000164617972868753	0.00202718269879021
ZNF263#10127	5	8.22184163701068	2.6606316672286e-05	0.000571403887916282

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.