Coexpression cluster:C4676

Full id: C4676_giant_Lens_embryonic_Preadipocyte_Iris_Fibroblast_blood

Phase1 CAGE Peaks

Hg19::chr7:23387355..23387366,-	p8@IGF2BP3
Hg19::chr7:23387369..23387401,-	p4@IGF2BP3
Hg19::chr7:23387403..23387438,-	p3@IGF2BP3

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><br>

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Cell Type

Ontology term	p-value	n
animal cell	1.02e-14	679
eukaryotic cell	1.02e-14	679
mesodermal cell	2.22e-14	121
native cell	2.77e-14	722
somatic cell	1.43e-10	588
lining cell	1.74e-10	58
barrier cell	1.74e-10	58
endothelial cell of vascular tree	5.57e-10	24
endothelial cell	1.08e-09	36
embryonic cell	1.26e-09	250
vascular associated smooth muscle cell	3.93e-09	32
smooth muscle cell	1.61e-08	43
smooth muscle myoblast	1.61e-08	43
blood vessel endothelial cell	1.93e-08	18
embryonic blood vessel endothelial progenitor cell	1.93e-08	18
squamous epithelial cell	1.49e-07	63

Uber Anatomy

Ontology term	p-value	n
cardiovascular system	1.36e-22	109
circulatory system	2.99e-21	112
vasculature	5.58e-18	78
vascular system	5.58e-18	78
artery	5.60e-16	42
arterial blood vessel	5.60e-16	42
arterial system	5.60e-16	42
vessel	4.11e-14	68
epithelial tube open at both ends	4.73e-14	59
blood vessel	4.73e-14	59
blood vasculature	4.73e-14	59
vascular cord	4.73e-14	59
systemic artery	2.88e-13	33
systemic arterial system	2.88e-13	33
splanchnic layer of lateral plate mesoderm	3.37e-13	83
mesoderm	6.90e-13	315
mesoderm-derived structure	6.90e-13	315
presumptive mesoderm	6.90e-13	315
lateral plate mesoderm	3.49e-12	203
aorta	1.31e-09	21
aortic system	1.31e-09	21
blood vessel endothelium	1.93e-08	18
endothelium	1.93e-08	18
cardiovascular system endothelium	1.93e-08	18
anatomical system	4.14e-08	624
anatomical group	6.54e-08	625
simple squamous epithelium	3.12e-07	22
musculoskeletal system	9.18e-07	167

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115800124609537
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322429324256664
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168464013714256
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901751708052168
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000372624025808655
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00446386105599947
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000682697549648549
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157661882933712
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000859675496153863
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109424536837478
STAT2#6773	3	65.2637711864407	3.59360517547754e-06	0.000118582158269099
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645449592151421
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249460737102472
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.0061887507157566
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331198450145803

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.