Coexpression cluster:C606

Full id: C606_Endothelial_extraskeletal_Smooth_mesothelioma_Lymphatic_Fibroblast_lung

Phase1 CAGE Peaks

Hg19::chr4:145566841..145566862,+	p10@HHIP
Hg19::chr4:145566874..145566889,+	p15@HHIP
Hg19::chr4:145566965..145566978,-	p2@ENST00000503066
Hg19::chr4:145567278..145567296,+	p3@HHIP
Hg19::chr4:145567297..145567355,+	p1@HHIP
Hg19::chr4:145567356..145567368,+	p7@HHIP
Hg19::chr4:145567374..145567390,+	p6@HHIP
Hg19::chr4:145567391..145567425,+	p4@HHIP
Hg19::chr4:145567426..145567455,+	p5@HHIP
Hg19::chr4:145567461..145567482,+	p9@HHIP
Hg19::chr4:145567538..145567544,+	p13@HHIP
Hg19::chr4:145567563..145567572,+	p8@HHIP
Hg19::chr4:145608930..145608933,+	p@chr4:145608930..145608933 +
Hg19::chr4:145629311..145629322,+	p17@HHIP
Hg19::chr4:145662551..145662554,+	p@chr4:145662551..145662554 +

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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GO ID	GO name	FDR corrected p-value
GO:0045879	negative regulation of smoothened signaling pathway	0.00156010832450253
GO:0040036	regulation of fibroblast growth factor receptor signaling pathway	0.0023401624867538
GO:0008589	regulation of smoothened signaling pathway	0.00364025275717257
GO:0007224	smoothened signaling pathway	0.00442030691942384
GO:0008543	fibroblast growth factor receptor signaling pathway	0.00442030691942384
GO:0007405	neuroblast proliferation	0.00442030691942384
GO:0009953	dorsal/ventral pattern formation	0.00624043329801013
GO:0030324	lung development	0.00745385088373431
GO:0030323	respiratory tube development	0.00745385088373431
GO:0003002	regionalization	0.013572942423172
GO:0009968	negative regulation of signal transduction	0.0147501150680239
GO:0035295	tube development	0.0148810332491011
GO:0007389	pattern specification process	0.0148810332491011
GO:0009986	cell surface	0.0164925737161696
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0218415165430354
GO:0048699	generation of neurons	0.0235966384081008
GO:0022008	neurogenesis	0.0240440224129214
GO:0007167	enzyme linked receptor protein signaling pathway	0.0260018054083755
GO:0009887	organ morphogenesis	0.0297241691299956

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
mesodermal cell	3.07e-22	119
endothelial cell of vascular tree	4.64e-17	24
vascular associated smooth muscle cell	3.42e-15	32
endothelial cell	1.41e-14	35
blood vessel endothelial cell	1.24e-13	18
embryonic blood vessel endothelial progenitor cell	1.24e-13	18
meso-epithelial cell	1.94e-13	44
contractile cell	3.17e-13	59
muscle precursor cell	6.15e-13	57
myoblast	6.15e-13	57
multi-potent skeletal muscle stem cell	6.15e-13	57
non-terminally differentiated cell	9.42e-13	180
smooth muscle cell	3.62e-12	42
smooth muscle myoblast	3.62e-12	42
muscle cell	6.37e-12	54
electrically responsive cell	3.44e-10	60
electrically active cell	3.44e-10	60
lining cell	2.14e-09	57
barrier cell	2.14e-09	57
endothelial cell of artery	8.55e-08	9

Uber Anatomy

Ontology term	p-value	n
tube	2.17e-42	194
anatomical conduit	1.50e-37	241
anatomical cluster	6.09e-35	286
vasculature	1.05e-34	79
vascular system	1.05e-34	79
cell layer	1.17e-33	312
epithelium	1.25e-32	309
vessel	2.88e-32	69
blood vessel	4.05e-30	60
epithelial tube open at both ends	4.05e-30	60
blood vasculature	4.05e-30	60
vascular cord	4.05e-30	60
splanchnic layer of lateral plate mesoderm	7.79e-29	84
epithelial tube	2.83e-28	118
cardiovascular system	9.59e-26	110
circulatory system	2.17e-24	113
artery	1.10e-23	42
arterial blood vessel	1.10e-23	42
arterial system	1.10e-23	42
systemic artery	1.35e-18	33
systemic arterial system	1.35e-18	33
regional part of brain	4.61e-17	59
neural tube	4.84e-17	57
neural rod	4.84e-17	57
future spinal cord	4.84e-17	57
neural keel	4.84e-17	57
unilaminar epithelium	1.45e-16	138
brain	2.54e-16	69
future brain	2.54e-16	69
central nervous system	5.83e-16	82
regional part of nervous system	1.47e-15	94
nervous system	1.47e-15	94
organism subdivision	1.16e-14	365
neural plate	1.26e-14	86
presumptive neural plate	1.26e-14	86
multi-tissue structure	5.04e-14	347
neurectoderm	8.16e-14	90
muscle tissue	1.02e-13	63
musculature	1.02e-13	63
musculature of body	1.02e-13	63
endothelium	1.24e-13	18
blood vessel endothelium	1.24e-13	18
cardiovascular system endothelium	1.24e-13	18
skeletal muscle tissue	3.64e-13	61
striated muscle tissue	3.64e-13	61
myotome	3.64e-13	61
multi-cellular organism	2.60e-12	659
regional part of forebrain	2.63e-12	41
forebrain	2.63e-12	41
future forebrain	2.63e-12	41
gray matter	3.14e-12	34
brain grey matter	3.14e-12	34
telencephalon	3.37e-12	34
aorta	4.07e-12	21
aortic system	4.07e-12	21
anterior neural tube	5.23e-12	42
adult organism	6.57e-12	115
regional part of telencephalon	8.23e-12	33
dermomyotome	1.29e-11	70
cerebral hemisphere	3.11e-11	32
anatomical system	3.12e-11	625
anatomical group	5.31e-11	626
trunk mesenchyme	8.16e-11	143
squamous epithelium	8.64e-11	25
simple squamous epithelium	1.02e-10	22
embryo	1.79e-10	612
pre-chordal neural plate	2.89e-10	61
somite	6.36e-10	83
paraxial mesoderm	6.36e-10	83
presomitic mesoderm	6.36e-10	83
presumptive segmental plate	6.36e-10	83
trunk paraxial mesoderm	6.36e-10	83
presumptive paraxial mesoderm	6.36e-10	83
embryonic structure	8.06e-10	605
developing anatomical structure	8.06e-10	605
germ layer	9.95e-10	604
embryonic tissue	9.95e-10	604
presumptive structure	9.95e-10	604

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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No analysis results for this cluster

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.