Coexpression cluster:C4206

Full id: C4206_Smooth_Keratinocyte_mesenchymal_Fibroblast_Bronchial_mucinous_Tracheal

Phase1 CAGE Peaks

Hg19::chr2:239335353..239335391,+	p4@ASB1
Hg19::chr2:239335396..239335448,+	p3@ASB1
Hg19::chr2:239335449..239335460,+	p7@ASB1

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
animal cell	1.72e-23	679
eukaryotic cell	1.72e-23	679
somatic cell	1.65e-20	591
native cell	7.41e-18	722
mesodermal cell	9.44e-16	119
non-terminally differentiated cell	1.83e-14	180
vascular associated smooth muscle cell	2.22e-13	32
muscle precursor cell	4.20e-13	57
myoblast	4.20e-13	57
multi-potent skeletal muscle stem cell	4.20e-13	57
somatic stem cell	8.89e-13	436
fibroblast	9.69e-13	75
muscle cell	1.28e-12	54
embryonic cell	3.81e-12	248
multi fate stem cell	1.03e-11	430
smooth muscle cell	1.11e-11	42
smooth muscle myoblast	1.11e-11	42
stem cell	3.85e-11	444
contractile cell	4.01e-11	59
electrically responsive cell	7.17e-09	60
electrically active cell	7.17e-09	60
cardiocyte	8.02e-08	16
respiratory epithelial cell	7.47e-07	13
aortic smooth muscle cell	7.62e-07	10
CD14-positive, CD16-negative classical monocyte	7.85e-07	42

Uber Anatomy

Ontology term	p-value	n
artery	2.37e-21	42
arterial blood vessel	2.37e-21	42
arterial system	2.37e-21	42
blood vessel	7.55e-18	60
epithelial tube open at both ends	7.55e-18	60
blood vasculature	7.55e-18	60
vascular cord	7.55e-18	60
systemic artery	8.38e-18	33
systemic arterial system	8.38e-18	33
vessel	3.02e-17	69
splanchnic layer of lateral plate mesoderm	3.22e-17	84
vasculature	5.78e-17	79
vascular system	5.78e-17	79
epithelial tube	3.10e-16	118
mesoderm	2.28e-13	448
mesoderm-derived structure	2.28e-13	448
presumptive mesoderm	2.28e-13	448
musculoskeletal system	3.13e-13	167
unilaminar epithelium	4.46e-13	138
cardiovascular system	1.16e-12	110
dermomyotome	3.47e-12	70
multilaminar epithelium	5.02e-12	82
circulatory system	7.91e-12	113
skeletal muscle tissue	3.01e-11	61
striated muscle tissue	3.01e-11	61
myotome	3.01e-11	61
anatomical system	3.62e-11	625
lateral plate mesoderm	3.89e-11	216
somite	4.55e-11	83
paraxial mesoderm	4.55e-11	83
presomitic mesoderm	4.55e-11	83
presumptive segmental plate	4.55e-11	83
trunk paraxial mesoderm	4.55e-11	83
presumptive paraxial mesoderm	4.55e-11	83
anatomical group	5.59e-11	626
aorta	1.30e-10	21
aortic system	1.30e-10	21
muscle tissue	2.35e-10	63
musculature	2.35e-10	63
musculature of body	2.35e-10	63
trunk mesenchyme	5.86e-10	143
multi-cellular organism	1.78e-09	659
trunk	4.78e-08	216
epithelium	1.39e-07	309
cell layer	3.63e-07	312
germ layer	5.21e-07	604
embryonic tissue	5.21e-07	604
presumptive structure	5.21e-07	604
epiblast (generic)	5.21e-07	604
embryonic structure	6.50e-07	605
developing anatomical structure	6.50e-07	605
blood vessel smooth muscle	7.62e-07	10
arterial system smooth muscle	7.62e-07	10
artery smooth muscle tissue	7.62e-07	10
aorta smooth muscle tissue	7.62e-07	10

Disease

Ontology term	p-value	n
ovarian cancer	4.06e-07	14

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326301410095763
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321456185130922
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463529884760566
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256033261301454
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763715088083155
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154461344790481
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270169505001171
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173283031415987
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769349953736763
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485528915472919
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248790935961074
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617165854762321

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.