Coexpression cluster:C2373

Full id: C2373_Mesenchymal_Renal_leiomyoblastoma_Hepatic_Pericytes_Fibroblast_Smooth

Phase1 CAGE Peaks

Hg19::chr16:447209..447225,+	p2@NME4
Hg19::chr16:447226..447242,+	p3@NME4
Hg19::chr16:447255..447266,+	p4@NME4
Hg19::chr16:447267..447272,+	p6@NME4

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	2.18e-32	180
mesodermal cell	2.73e-23	119
embryonic cell	1.60e-22	248
contractile cell	3.13e-21	59
muscle precursor cell	1.67e-19	57
myoblast	1.67e-19	57
multi-potent skeletal muscle stem cell	1.67e-19	57
muscle cell	4.70e-19	54
smooth muscle cell	2.21e-18	42
smooth muscle myoblast	2.21e-18	42
electrically responsive cell	2.59e-17	60
electrically active cell	2.59e-17	60
somatic cell	1.15e-15	591
vascular associated smooth muscle cell	5.03e-15	32
animal cell	1.91e-13	679
eukaryotic cell	1.91e-13	679
fibroblast	1.02e-10	75

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	2.90e-22	143
trunk	8.10e-19	216
somite	1.13e-18	83
paraxial mesoderm	1.13e-18	83
presomitic mesoderm	1.13e-18	83
presumptive segmental plate	1.13e-18	83
trunk paraxial mesoderm	1.13e-18	83
presumptive paraxial mesoderm	1.13e-18	83
epithelial tube	4.27e-18	118
dermomyotome	5.35e-18	70
vasculature	6.84e-18	79
vascular system	6.84e-18	79
multilaminar epithelium	1.07e-17	82
skeletal muscle tissue	3.04e-17	61
striated muscle tissue	3.04e-17	61
myotome	3.04e-17	61
muscle tissue	3.15e-17	63
musculature	3.15e-17	63
musculature of body	3.15e-17	63
unilaminar epithelium	9.58e-17	138
splanchnic layer of lateral plate mesoderm	2.99e-16	84
blood vessel	1.02e-14	60
epithelial tube open at both ends	1.02e-14	60
blood vasculature	1.02e-14	60
vascular cord	1.02e-14	60
vessel	1.12e-14	69
artery	1.16e-13	42
arterial blood vessel	1.16e-13	42
arterial system	1.16e-13	42
cardiovascular system	1.37e-12	110
circulatory system	2.72e-12	113
mesenchyme	1.61e-11	238
entire embryonic mesenchyme	1.61e-11	238
organism subdivision	4.12e-11	365
cell layer	1.99e-10	312
systemic artery	2.55e-10	33
systemic arterial system	2.55e-10	33
epithelium	3.36e-10	309
subdivision of trunk	1.37e-08	113
multi-tissue structure	3.23e-07	347

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511766823784039
CTCFL#140690	4	19.7464743589744	6.5732084880439e-06	0.000192728613498825
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106428165847327
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00996354711573236
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101382572613117
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154431240752395
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185844393224963
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00247982452381977
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391373784539339
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.0044356281540444
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795583669416504
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321863046678024
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106731614310097
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346265106527126

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.