Coexpression cluster:C3273

Full id: C3273_osteosarcoma_endometrial_embryonic_astrocytoma_mucinous_Myoblast_prostate

Phase1 CAGE Peaks

Hg19::chr12:27485762..27485776,+	p3@ARNTL2
Hg19::chr12:27485785..27485816,+	p1@ARNTL2
Hg19::chr12:27485823..27485868,+	p2@ARNTL2

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	1.15e-16	254
embryonic cell	6.06e-14	248
endo-epithelial cell	4.59e-09	43
animal cell	5.56e-09	679
eukaryotic cell	5.56e-09	679
squamous epithelial cell	7.12e-09	62
mesodermal cell	2.08e-08	119
endodermal cell	2.75e-08	59
vascular associated smooth muscle cell	1.48e-07	32
endothelial cell of vascular tree	3.60e-07	24

Uber Anatomy

Ontology term	p-value	n
vessel	1.07e-11	69
blood vessel	1.39e-10	60
epithelial tube open at both ends	1.39e-10	60
blood vasculature	1.39e-10	60
vascular cord	1.39e-10	60
artery	9.28e-10	42
arterial blood vessel	9.28e-10	42
arterial system	9.28e-10	42
unilaminar epithelium	1.21e-09	138
vasculature	1.42e-09	79
vascular system	1.42e-09	79
epithelial tube	1.26e-07	118
anatomical group	2.12e-07	626
systemic artery	2.76e-07	33
systemic arterial system	2.76e-07	33
anatomical conduit	3.44e-07	241
trunk mesenchyme	3.61e-07	143
epithelium	3.78e-07	309
anatomical system	3.89e-07	625
cell layer	4.16e-07	312

Disease

Ontology term	p-value	n
carcinoma	1.93e-09	106
disease of cellular proliferation	4.37e-08	239
cancer	5.25e-08	235
cell type cancer	1.75e-07	143

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324039915174307
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436018374321613
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320883379361278
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460547107591939
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268835959084821
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613730029412916
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032827567561927
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108997765716542

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.