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	5.85e-16	427
classical monocyte	2.36e-15	42
CD14-positive, CD16-negative classical monocyte	2.36e-15	42
somatic stem cell	2.58e-15	433
stem cell	1.75e-14	441
muscle precursor cell	1.08e-13	58
myoblast	1.08e-13	58
multi-potent skeletal muscle stem cell	1.08e-13	58
contractile cell	2.57e-13	59
muscle cell	9.71e-13	55
defensive cell	1.80e-12	48
phagocyte	1.80e-12	48
smooth muscle cell	6.54e-11	43
smooth muscle myoblast	6.54e-11	43
electrically responsive cell	1.09e-10	61
electrically active cell	1.09e-10	61
somatic cell	2.16e-10	588
macrophage dendritic cell progenitor	6.51e-10	61
vascular associated smooth muscle cell	1.23e-09	32
monopoietic cell	1.34e-09	59
monocyte	1.34e-09	59
monoblast	1.34e-09	59
promonocyte	1.34e-09	59
non-terminally differentiated cell	4.49e-09	106
animal cell	8.60e-09	679
eukaryotic cell	8.60e-09	679
granulocyte monocyte progenitor cell	2.22e-08	67
myeloid lineage restricted progenitor cell	7.46e-08	66
mesenchymal cell	4.06e-07	354

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	1.31e-14	167
mesoderm	8.75e-13	315
mesoderm-derived structure	8.75e-13	315
presumptive mesoderm	8.75e-13	315
skeletal muscle tissue	3.05e-12	62
striated muscle tissue	3.05e-12	62
myotome	3.05e-12	62
epithelial vesicle	5.56e-12	78
muscle tissue	1.37e-11	64
musculature	1.37e-11	64
musculature of body	1.37e-11	64
somite	2.18e-11	71
presomitic mesoderm	2.18e-11	71
presumptive segmental plate	2.18e-11	71
dermomyotome	2.18e-11	71
trunk paraxial mesoderm	2.18e-11	71
paraxial mesoderm	4.19e-11	72
presumptive paraxial mesoderm	4.19e-11	72
dense mesenchyme tissue	7.88e-11	73
female gonad	4.76e-09	13
multilaminar epithelium	1.72e-08	83
systemic artery	3.30e-08	33
systemic arterial system	3.30e-08	33
left ovary	9.37e-08	4
bone marrow	2.66e-07	76
female reproductive organ	4.13e-07	37
female reproductive system	4.13e-07	37
bone element	5.26e-07	82

Disease

Ontology term	p-value	n
ovarian cancer	5.20e-15	14
female reproductive organ cancer	9.40e-09	27
reproductive organ cancer	7.15e-08	29
benign neoplasm	9.72e-07	4

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.