Coexpression cluster:C2918

Full id: C2918_Mast_mesothelioma_spindle_mesodermal_myxofibrosarcoma_lens_neurofibroma

Phase1 CAGE Peaks

Hg19::chr8:13133974..13133985,-	p13@DLC1
Hg19::chr8:13134001..13134011,-	p14@DLC1
Hg19::chr8:13134015..13134038,-	p2@DLC1
Hg19::chr8:13134045..13134063,-	p5@DLC1

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	1.14e-23	180
fibroblast	5.36e-21	75
mesodermal cell	5.85e-20	119
endothelial cell of vascular tree	4.33e-12	24
endothelial cell	1.58e-11	35
contractile cell	8.83e-11	59
muscle precursor cell	8.83e-11	57
myoblast	8.83e-11	57
multi-potent skeletal muscle stem cell	8.83e-11	57
blood vessel endothelial cell	4.41e-10	18
embryonic blood vessel endothelial progenitor cell	4.41e-10	18
skin fibroblast	4.89e-10	23
embryonic cell	5.42e-10	248
muscle cell	6.03e-10	54
meso-epithelial cell	1.20e-09	44
lining cell	2.07e-09	57
barrier cell	2.07e-09	57
smooth muscle cell	2.35e-08	42
smooth muscle myoblast	2.35e-08	42
vascular associated smooth muscle cell	3.73e-08	32
electrically responsive cell	3.24e-07	60
electrically active cell	3.24e-07	60

Uber Anatomy

Ontology term	p-value	n
cell layer	6.81e-24	312
vasculature	9.16e-24	79
vascular system	9.16e-24	79
epithelial tube	1.06e-22	118
epithelium	1.18e-22	309
organism subdivision	1.94e-22	365
anatomical cluster	6.27e-21	286
anatomical conduit	2.77e-20	241
vessel	8.05e-20	69
tube	1.50e-18	194
blood vessel	1.08e-17	60
epithelial tube open at both ends	1.08e-17	60
blood vasculature	1.08e-17	60
vascular cord	1.08e-17	60
trunk mesenchyme	2.43e-17	143
splanchnic layer of lateral plate mesoderm	2.67e-17	84
unilaminar epithelium	1.43e-16	138
circulatory system	3.66e-16	113
cardiovascular system	4.97e-16	110
multi-cellular organism	3.17e-14	659
artery	3.34e-14	42
arterial blood vessel	3.34e-14	42
arterial system	3.34e-14	42
multi-tissue structure	3.35e-14	347
trunk	3.76e-14	216
somite	5.88e-14	83
paraxial mesoderm	5.88e-14	83
presomitic mesoderm	5.88e-14	83
presumptive segmental plate	5.88e-14	83
trunk paraxial mesoderm	5.88e-14	83
presumptive paraxial mesoderm	5.88e-14	83
anatomical system	3.44e-13	625
anatomical group	6.27e-13	626
dermomyotome	6.41e-13	70
multilaminar epithelium	3.01e-11	82
systemic artery	9.73e-11	33
systemic arterial system	9.73e-11	33
endothelium	4.41e-10	18
blood vessel endothelium	4.41e-10	18
cardiovascular system endothelium	4.41e-10	18
skeletal muscle tissue	4.58e-10	61
striated muscle tissue	4.58e-10	61
myotome	4.58e-10	61
muscle tissue	9.08e-10	63
musculature	9.08e-10	63
musculature of body	9.08e-10	63
surface structure	2.20e-09	95
simple squamous epithelium	4.50e-09	22
aorta	8.80e-09	21
aortic system	8.80e-09	21
integument	1.20e-08	45
integumental system	1.20e-08	45
mesenchyme	2.65e-08	238
entire embryonic mesenchyme	2.65e-08	238
squamous epithelium	2.87e-08	25
germ layer	3.09e-07	604
embryonic tissue	3.09e-07	604
presumptive structure	3.09e-07	604
epiblast (generic)	3.09e-07	604
embryonic structure	3.60e-07	605
developing anatomical structure	3.60e-07	605
skin of body	4.05e-07	40

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	4	7.97114762582482	0.000247638578809083	0.0026881951493859
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00129391927327857
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106838646520209
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161302944480083
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00435594550102458
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00195561573734488
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.000304467743067854
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.0010737765381205
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000628855342439093
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186685278029515
HNF4A#3172	4	23.1322903629537	3.48990320893214e-06	0.000115892528215473
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000745572901317352
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392748014988338
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.0013006033266186
REST#5978	4	9.65002871612802	0.000115282561421917	0.0015761219311878
RXRA#6256	4	20.0746171391333	6.1537798808435e-06	0.000182635583113218
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00685888146587309
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323419323980931
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245124702028832
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115813411753681
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00509266202487915
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00250081075044441

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.