Coexpression cluster:C4699

Full id: C4699_Mesenchymal_Urothelial_vagina_Renal_MCF7_salivary_skeletal

Phase1 CAGE Peaks

Hg19::chr7:75931982..75932005,+	p1@HSPB1
Hg19::chr7:75932326..75932393,-	p@chr7:75932326..75932393 -
Hg19::chrX:49090623..49090648,-	p2@HSPB1P2

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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GO ID	GO name	FDR corrected p-value
GO:0006446	regulation of translational initiation	0.0362062875309078
GO:0006986	response to unfolded protein	0.0362062875309078
GO:0051789	response to protein stimulus	0.0362062875309078
GO:0006413	translational initiation	0.0362062875309078
GO:0022618	protein-RNA complex assembly	0.0362062875309078
GO:0009986	cell surface	0.0362062875309078
GO:0006916	anti-apoptosis	0.0362062875309078
GO:0006417	regulation of translation	0.0362062875309078
GO:0031326	regulation of cellular biosynthetic process	0.0362062875309078
GO:0009889	regulation of biosynthetic process	0.0362062875309078
GO:0043066	negative regulation of apoptosis	0.0362062875309078
GO:0043069	negative regulation of programmed cell death	0.0362062875309078
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0362062875309078
GO:0009607	response to biotic stimulus	0.0394968125010513
GO:0051674	localization of cell	0.0458005857765218
GO:0006928	cell motility	0.0458005857765218
GO:0051246	regulation of protein metabolic process	0.0474958616438451

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><br>

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Cell Type

Ontology term	p-value	n
embryonic cell	1.68e-14	248
mesodermal cell	4.01e-14	119
non-terminally differentiated cell	1.20e-10	180
endothelial cell	7.83e-09	35
endothelial cell of vascular tree	1.12e-08	24
epithelial cell	1.78e-08	254
lining cell	4.05e-08	57
barrier cell	4.05e-08	57
contractile cell	8.78e-08	59
muscle precursor cell	1.31e-07	57
myoblast	1.31e-07	57
multi-potent skeletal muscle stem cell	1.31e-07	57
meso-epithelial cell	3.22e-07	44
blood vessel endothelial cell	4.62e-07	18
embryonic blood vessel endothelial progenitor cell	4.62e-07	18
muscle cell	4.78e-07	54

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	3.99e-17	659
splanchnic layer of lateral plate mesoderm	2.55e-16	84
organism subdivision	3.28e-16	365
trunk	9.61e-16	216
vessel	4.99e-15	69
vasculature	2.38e-14	79
vascular system	2.38e-14	79
blood vessel	2.96e-13	60
epithelial tube open at both ends	2.96e-13	60
blood vasculature	2.96e-13	60
vascular cord	2.96e-13	60
mesenchyme	5.01e-13	238
entire embryonic mesenchyme	5.01e-13	238
epithelial tube	5.97e-13	118
anatomical system	3.72e-12	625
anatomical group	5.61e-12	626
trunk mesenchyme	6.18e-12	143
unilaminar epithelium	1.81e-11	138
epithelium	6.89e-11	309
multi-tissue structure	7.59e-11	347
cell layer	1.47e-10	312
multilaminar epithelium	1.69e-10	82
circulatory system	2.18e-10	113
anatomical cluster	2.39e-10	286
anatomical conduit	3.42e-10	241
surface structure	1.01e-09	95
muscle tissue	1.18e-09	63
musculature	1.18e-09	63
musculature of body	1.18e-09	63
somite	1.30e-09	83
paraxial mesoderm	1.30e-09	83
presomitic mesoderm	1.30e-09	83
presumptive segmental plate	1.30e-09	83
trunk paraxial mesoderm	1.30e-09	83
presumptive paraxial mesoderm	1.30e-09	83
skeletal muscle tissue	2.22e-09	61
striated muscle tissue	2.22e-09	61
myotome	2.22e-09	61
cardiovascular system	2.42e-09	110
dermomyotome	2.57e-09	70
compound organ	4.23e-09	69
subdivision of trunk	1.70e-08	113
mesoderm	4.45e-08	448
mesoderm-derived structure	4.45e-08	448
presumptive mesoderm	4.45e-08	448
artery	5.26e-08	42
arterial blood vessel	5.26e-08	42
arterial system	5.26e-08	42
simple squamous epithelium	1.70e-07	22
squamous epithelium	3.91e-07	25
embryo	4.57e-07	612
endothelium	4.62e-07	18
blood vessel endothelium	4.62e-07	18
cardiovascular system endothelium	4.62e-07	18
embryonic structure	6.13e-07	605
developing anatomical structure	6.13e-07	605

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
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460804059440161

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.