Coexpression cluster:C504

Full id: C504_leiomyoma_Lens_Ciliary_mesenchymal_Smooth_Mesothelial_Renal

Phase1 CAGE Peaks

Hg19::chr3:98515870..98515887,-	p2@DCBLD2
Hg19::chr3:98515943..98515954,-	p15@DCBLD2
Hg19::chr3:98516110..98516123,-	p5@DCBLD2
Hg19::chr3:98516909..98516965,-	p6@DCBLD2
Hg19::chr3:98516991..98517004,-	p22@DCBLD2
Hg19::chr3:98517010..98517033,-	p14@DCBLD2
Hg19::chr3:98517248..98517268,-	p27@DCBLD2
Hg19::chr3:98517295..98517325,-	p11@DCBLD2
Hg19::chr3:98517628..98517642,-	p10@DCBLD2
Hg19::chr3:98517866..98517882,-	p26@DCBLD2
Hg19::chr3:98518027..98518049,-	p9@DCBLD2
Hg19::chr3:98518144..98518166,-	p7@DCBLD2
Hg19::chr3:98518582..98518608,-	p@chr3:98518582..98518608 -
Hg19::chr3:98518647..98518667,-	p@chr3:98518647..98518667 -
Hg19::chr3:98530363..98530400,-	p@chr3:98530363..98530400 -
Hg19::chr3:98531239..98531265,-	p12@DCBLD2
Hg19::chr3:98531283..98531302,-	p20@DCBLD2
Hg19::chr3:98536685..98536713,-	p8@DCBLD2
Hg19::chr3:98536722..98536741,-	p19@DCBLD2

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
embryonic cell	1.07e-31	248
non-terminally differentiated cell	4.11e-31	180
epithelial cell	9.39e-18	254
muscle precursor cell	2.64e-17	57
myoblast	2.64e-17	57
multi-potent skeletal muscle stem cell	2.64e-17	57
animal cell	2.87e-16	679
eukaryotic cell	2.87e-16	679
electrically responsive cell	8.13e-16	60
electrically active cell	8.13e-16	60
muscle cell	8.65e-16	54
mesodermal cell	1.27e-15	119
contractile cell	6.09e-15	59
smooth muscle cell	2.50e-13	42
smooth muscle myoblast	2.50e-13	42
vascular associated smooth muscle cell	6.12e-13	32
fibroblast	2.42e-10	75
ectodermal cell	1.06e-09	71
neurectodermal cell	6.05e-08	59
native cell	1.38e-07	722
somatic cell	3.72e-07	591

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	1.43e-21	143
organism subdivision	3.44e-19	365
multilaminar epithelium	4.64e-19	82
cell layer	3.67e-18	312
epithelium	3.70e-18	309
trunk	1.58e-17	216
somite	1.21e-16	83
paraxial mesoderm	1.21e-16	83
presomitic mesoderm	1.21e-16	83
presumptive segmental plate	1.21e-16	83
trunk paraxial mesoderm	1.21e-16	83
presumptive paraxial mesoderm	1.21e-16	83
dermomyotome	4.20e-16	70
multi-tissue structure	1.13e-15	347
skeletal muscle tissue	2.38e-15	61
striated muscle tissue	2.38e-15	61
myotome	2.38e-15	61
unilaminar epithelium	5.98e-15	138
mesenchyme	1.29e-14	238
entire embryonic mesenchyme	1.29e-14	238
muscle tissue	1.54e-14	63
musculature	1.54e-14	63
musculature of body	1.54e-14	63
epithelial tube	3.64e-14	118
multi-cellular organism	5.62e-13	659
artery	8.21e-12	42
arterial blood vessel	8.21e-12	42
arterial system	8.21e-12	42
anatomical system	1.50e-10	625
anatomical group	2.30e-10	626
systemic artery	9.77e-10	33
systemic arterial system	9.77e-10	33
vasculature	1.02e-09	79
vascular system	1.02e-09	79
embryo	1.31e-09	612
primordium	2.41e-09	168
embryonic structure	4.58e-09	605
developing anatomical structure	4.58e-09	605
germ layer	6.59e-09	604
embryonic tissue	6.59e-09	604
presumptive structure	6.59e-09	604
epiblast (generic)	6.59e-09	604
anatomical cluster	1.02e-08	286
blood vessel	2.72e-08	60
epithelial tube open at both ends	2.72e-08	60
blood vasculature	2.72e-08	60
vascular cord	2.72e-08	60
splanchnic layer of lateral plate mesoderm	2.92e-08	84
surface structure	5.87e-08	95
anatomical conduit	1.94e-07	241
vessel	2.20e-07	69
pigment epithelium of eye	4.07e-07	11

Disease

Ontology term	p-value	n
female reproductive organ cancer	1.33e-08	27
ovarian cancer	1.52e-08	14
reproductive organ cancer	1.59e-08	29

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.