Coexpression cluster:C964

Full id: C964_Nucleus_Anulus_meningioma_large_Olfactory_Chondrocyte_Mesothelial

Phase1 CAGE Peaks

Hg19::chrX:119694291..119694298,-	p21@CUL4B
Hg19::chrX:119694334..119694362,-	p5@CUL4B
Hg19::chrX:119694463..119694476,-	p17@CUL4B
Hg19::chrX:119694505..119694522,-	p8@CUL4B
Hg19::chrX:119694538..119694549,-	p20@CUL4B
Hg19::chrX:119694573..119694611,-	p2@CUL4B
Hg19::chrX:119694622..119694642,-	p3@CUL4B
Hg19::chrX:119694719..119694730,-	p14@CUL4B
Hg19::chrX:119694739..119694751,-	p12@CUL4B

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
non-terminally differentiated cell	7.85e-23	180
mesodermal cell	1.98e-17	119
fibroblast	2.22e-14	75
muscle precursor cell	1.30e-11	57
myoblast	1.30e-11	57
multi-potent skeletal muscle stem cell	1.30e-11	57
muscle cell	2.48e-10	54
electrically responsive cell	2.60e-09	60
electrically active cell	2.60e-09	60
skin fibroblast	7.31e-09	23
contractile cell	8.30e-09	59
mesothelial cell	2.12e-08	19
lining cell	4.23e-08	57
barrier cell	4.23e-08	57
smooth muscle cell	8.33e-08	42
smooth muscle myoblast	8.33e-08	42
vascular associated smooth muscle cell	1.76e-07	32

Uber Anatomy

Ontology term	p-value	n
cardiovascular system	3.60e-13	110
organism subdivision	3.60e-13	365
circulatory system	1.62e-12	113
unilaminar epithelium	2.08e-12	138
vasculature	5.64e-12	79
vascular system	5.64e-12	79
somite	8.21e-12	83
paraxial mesoderm	8.21e-12	83
presomitic mesoderm	8.21e-12	83
presumptive segmental plate	8.21e-12	83
trunk paraxial mesoderm	8.21e-12	83
presumptive paraxial mesoderm	8.21e-12	83
multi-tissue structure	4.78e-11	347
dermomyotome	1.04e-10	70
skeletal muscle tissue	1.30e-10	61
striated muscle tissue	1.30e-10	61
myotome	1.30e-10	61
muscle tissue	2.23e-10	63
musculature	2.23e-10	63
musculature of body	2.23e-10	63
anatomical cluster	4.20e-10	286
splanchnic layer of lateral plate mesoderm	6.32e-10	84
blood vessel	8.18e-10	60
epithelial tube open at both ends	8.18e-10	60
blood vasculature	8.18e-10	60
vascular cord	8.18e-10	60
vessel	1.11e-09	69
trunk	2.83e-09	216
trunk mesenchyme	3.97e-09	143
cell layer	2.68e-08	312
artery	2.86e-08	42
arterial blood vessel	2.86e-08	42
arterial system	2.86e-08	42
multilaminar epithelium	3.45e-08	82
systemic artery	3.78e-08	33
systemic arterial system	3.78e-08	33
epithelial tube	4.11e-08	118
epithelium	4.31e-08	309
mesenchyme	2.93e-07	238
entire embryonic mesenchyme	2.93e-07	238
anatomical conduit	4.06e-07	241

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	5	4.42841534768045	0.0025225868523706	0.0139883427989133
EGR1#1958	8	4.43393697316457	1.92853122912633e-05	0.000435489455218865
ELK4#2005	7	12.6277524010307	1.08190108922051e-07	6.31243954508943e-06
ETS1#2113	4	4.32389374320104	0.00918753673932392	0.0347482128455947
FOXA1#3169	5	6.15634430521414	0.00055192590587499	0.00471282721639098
FOXA2#3170	5	13.6835909737029	1.21001374207767e-05	0.000302979202131022
HEY1#23462	8	3.59120981609396	9.88548321897326e-05	0.00139254111398213
IRF1#3659	5	4.24286875197995	0.00306203286774801	0.0161464026393383
MXI1#4601	4	4.42736516833747	0.00844465741513493	0.032780210956301
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00729035417990706
SRF#6722	5	7.66509903453767	0.000196444781216345	0.00236174703642844
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395995532112675
USF1#7391	5	3.53416626511553	0.0069229675408181	0.02931154201952
USF2#7392	6	8.66146492337973	1.42236000274901e-05	0.000340398387550651

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.