Coexpression cluster:C2908

Full id: C2908_squamous_fibrous_large_mesenchymal_giant_Renal_serous

Phase1 CAGE Peaks

Hg19::chr7:93690316..93690375,+	p1@ENST00000438538
Hg19::chr7:93690403..93690432,+	p2@ENST00000438538
Hg19::chr7:93690435..93690467,+	p3@ENST00000438538
Hg19::chr7:93690805..93690815,+	p@chr7:93690805..93690815 +

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
multi fate stem cell	1.01e-25	430
somatic stem cell	1.05e-25	436
stem cell	3.36e-24	444
non-terminally differentiated cell	3.06e-21	180
muscle precursor cell	9.38e-21	57
myoblast	9.38e-21	57
multi-potent skeletal muscle stem cell	9.38e-21	57
muscle cell	2.92e-19	54
contractile cell	2.09e-18	59
somatic cell	5.83e-17	591
electrically responsive cell	7.93e-16	60
electrically active cell	7.93e-16	60
smooth muscle cell	1.58e-15	42
smooth muscle myoblast	1.58e-15	42
animal cell	2.19e-15	679
eukaryotic cell	2.19e-15	679
CD14-positive, CD16-negative classical monocyte	3.52e-15	42
vascular associated smooth muscle cell	6.58e-15	32
classical monocyte	2.12e-13	45
mesenchymal cell	1.76e-11	358
connective tissue cell	6.93e-11	365
native cell	9.31e-11	722
motile cell	2.35e-10	390
skin fibroblast	9.38e-09	23
macrophage dendritic cell progenitor	1.33e-08	65
monopoietic cell	1.66e-08	63
monocyte	1.66e-08	63
monoblast	1.66e-08	63
promonocyte	1.66e-08	63
fibroblast	2.36e-07	75
granulocyte monocyte progenitor cell	5.15e-07	71

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	1.65e-20	167
dermomyotome	1.06e-19	70
skeletal muscle tissue	2.54e-18	61
striated muscle tissue	2.54e-18	61
myotome	2.54e-18	61
somite	1.32e-17	83
paraxial mesoderm	1.32e-17	83
presomitic mesoderm	1.32e-17	83
presumptive segmental plate	1.32e-17	83
trunk paraxial mesoderm	1.32e-17	83
presumptive paraxial mesoderm	1.32e-17	83
muscle tissue	3.11e-17	63
musculature	3.11e-17	63
musculature of body	3.11e-17	63
multilaminar epithelium	2.73e-16	82
connective tissue	8.01e-11	375
trunk mesenchyme	1.12e-10	143
artery	9.65e-09	42
arterial blood vessel	9.65e-09	42
arterial system	9.65e-09	42
systemic artery	2.46e-08	33
systemic arterial system	2.46e-08	33
lateral plate mesoderm	4.04e-08	216
mesoderm	2.22e-07	448
mesoderm-derived structure	2.22e-07	448
presumptive mesoderm	2.22e-07	448
female gonad	3.08e-07	13
smooth muscle tissue	8.01e-07	15

Disease

Ontology term	p-value	n
ovarian cancer	9.55e-14	14
female reproductive organ cancer	1.05e-07	27
reproductive organ cancer	8.82e-07	29

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)
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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
BATF#10538	3	18.2683513442277	0.000268166010572129	0.00286839307436937
BCL11A#53335	3	21.2770913277053	0.000170483911460614	0.00208223239726758

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.