Coexpression cluster:C2156

Full id: C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair

Phase1 CAGE Peaks

Hg19::chr11:65687158..65687216,+	p4@DRAP1
Hg19::chr11:65687222..65687240,+	p7@DRAP1
Hg19::chr11:65687243..65687276,+	p8@DRAP1
Hg19::chr11:65687362..65687436,+	p3@DRAP1

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	3.08e-33	180
somatic cell	9.26e-28	591
mesodermal cell	1.41e-22	119
muscle precursor cell	4.93e-20	57
myoblast	4.93e-20	57
multi-potent skeletal muscle stem cell	4.93e-20	57
contractile cell	4.80e-19	59
muscle cell	1.76e-18	54
animal cell	2.83e-18	679
eukaryotic cell	2.83e-18	679
fibroblast	3.50e-18	75
smooth muscle cell	2.96e-17	42
smooth muscle myoblast	2.96e-17	42
native cell	3.18e-17	722
electrically responsive cell	3.74e-15	60
electrically active cell	3.74e-15	60
vascular associated smooth muscle cell	5.11e-15	32
embryonic cell	3.57e-14	248
stem cell	2.12e-13	444
somatic stem cell	2.13e-13	436
multi fate stem cell	3.10e-13	430
skin fibroblast	6.51e-09	23

Uber Anatomy

Ontology term	p-value	n
somite	2.01e-23	83
paraxial mesoderm	2.01e-23	83
presomitic mesoderm	2.01e-23	83
presumptive segmental plate	2.01e-23	83
trunk paraxial mesoderm	2.01e-23	83
presumptive paraxial mesoderm	2.01e-23	83
multilaminar epithelium	6.65e-20	82
dermomyotome	9.87e-20	70
artery	1.01e-17	42
arterial blood vessel	1.01e-17	42
arterial system	1.01e-17	42
skeletal muscle tissue	5.51e-16	61
striated muscle tissue	5.51e-16	61
myotome	5.51e-16	61
systemic artery	5.62e-15	33
systemic arterial system	5.62e-15	33
muscle tissue	1.55e-14	63
musculature	1.55e-14	63
musculature of body	1.55e-14	63
vessel	3.31e-14	69
blood vessel	7.41e-14	60
epithelial tube open at both ends	7.41e-14	60
blood vasculature	7.41e-14	60
vascular cord	7.41e-14	60
trunk mesenchyme	8.32e-14	143
vasculature	9.93e-14	79
vascular system	9.93e-14	79
surface structure	4.76e-13	95
splanchnic layer of lateral plate mesoderm	1.86e-11	84
cardiovascular system	7.02e-11	110
integument	1.19e-09	45
integumental system	1.19e-09	45
circulatory system	1.94e-09	113
unilaminar epithelium	2.25e-09	138
trunk	7.92e-09	216
skin of body	2.09e-08	40
aorta	5.07e-08	21
aortic system	5.07e-08	21
epithelial tube	9.95e-08	118
organism subdivision	9.14e-07	365

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
BCL11A#53335	2	14.1847275518035	0.00710832858529874	0.0296149165916713
BCL3#602	2	17.2735514018692	0.00483449420807607	0.0226711750975375
BCLAF1#9774	3	16.2394857075914	0.00038025670676648	0.00376539586593196
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487028434795308
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995151457287175
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240352684964235
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101285165469551
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418714109597739
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191980298298308
FOSL1#8061	3	29.7851847872798	6.26173959487248e-05	0.00102487043025997
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378401301338831
GATA3#2625	2	13.618258178603	0.0076966520809334	0.03168804536132
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992127702119396
HNF4A#3172	2	11.5661451814768	0.0105758568176249	0.0390597605974938
HNF4G#3174	3	21.5650668948351	0.000163803242129261	0.00203538926885638
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386696970156678
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00484526829584958
MEF2C#4208	2	20.655677246312	0.00340257057944504	0.0173550043341796
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186234769543646
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00885793873393624
NR2C2#7182	3	24.4609581789307	0.000112590606343803	0.00155499211001593
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.0044322751678705
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428216007613201
SMC3#9126	3	11.2836996336996	0.00111580236686805	0.00765457720660357
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328022278051251
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00404819939797118
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.0089810429523988
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158574227613622

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.