Coexpression cluster:C1350

Full id: C1350_neuroectodermal_neuroblastoma_Melanocyte_Smooth_leiomyoma_hepatoma_mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:69455914..69455932,+	p1@CCND1
Hg19::chr11:69457902..69457918,+	p@chr11:69457902..69457918 +
Hg19::chr11:69457929..69457972,+	p@chr11:69457929..69457972 +
Hg19::chr11:69458592..69458678,+	p4@CCND1
Hg19::chr11:69462821..69462870,+	p6@CCND1
Hg19::chr11:69466948..69466985,+	p10@CCND1

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	8.29e-30	180
embryonic cell	6.46e-28	248
mesodermal cell	2.38e-18	119
smooth muscle cell	8.16e-17	42
smooth muscle myoblast	8.16e-17	42
vascular associated smooth muscle cell	3.61e-16	32
epithelial cell	1.15e-14	254
muscle precursor cell	2.72e-14	57
myoblast	2.72e-14	57
multi-potent skeletal muscle stem cell	2.72e-14	57
fibroblast	9.50e-14	75
contractile cell	3.22e-13	59
muscle cell	5.59e-13	54
animal cell	1.66e-12	679
eukaryotic cell	1.66e-12	679
electrically responsive cell	3.28e-11	60
electrically active cell	3.28e-11	60
aortic smooth muscle cell	2.61e-07	10
somatic cell	8.32e-07	591

Uber Anatomy

Ontology term	p-value	n
trunk	1.48e-24	216
trunk mesenchyme	3.02e-22	143
epithelial tube	4.32e-20	118
vasculature	9.60e-20	79
vascular system	9.60e-20	79
vessel	1.26e-19	69
organism subdivision	6.36e-19	365
blood vessel	9.91e-18	60
epithelial tube open at both ends	9.91e-18	60
blood vasculature	9.91e-18	60
vascular cord	9.91e-18	60
artery	2.08e-17	42
arterial blood vessel	2.08e-17	42
arterial system	2.08e-17	42
mesenchyme	4.05e-16	238
entire embryonic mesenchyme	4.05e-16	238
unilaminar epithelium	4.79e-16	138
somite	9.47e-16	83
paraxial mesoderm	9.47e-16	83
presomitic mesoderm	9.47e-16	83
presumptive segmental plate	9.47e-16	83
trunk paraxial mesoderm	9.47e-16	83
presumptive paraxial mesoderm	9.47e-16	83
systemic artery	5.47e-15	33
systemic arterial system	5.47e-15	33
splanchnic layer of lateral plate mesoderm	8.35e-15	84
multi-cellular organism	1.40e-14	659
dermomyotome	1.66e-14	70
multilaminar epithelium	1.68e-14	82
skeletal muscle tissue	2.32e-12	61
striated muscle tissue	2.32e-12	61
myotome	2.32e-12	61
cell layer	6.57e-12	312
muscle tissue	9.78e-12	63
musculature	9.78e-12	63
musculature of body	9.78e-12	63
epithelium	1.12e-11	309
multi-tissue structure	2.30e-11	347
surface structure	4.56e-11	95
cardiovascular system	2.03e-10	110
anatomical system	5.73e-10	625
anatomical conduit	6.23e-10	241
circulatory system	7.33e-10	113
anatomical group	9.46e-10	626
subdivision of trunk	1.17e-09	113
anatomical cluster	2.97e-09	286
aorta	1.16e-08	21
aortic system	1.16e-08	21
integument	1.32e-07	45
integumental system	1.32e-07	45
blood vessel smooth muscle	2.61e-07	10
arterial system smooth muscle	2.61e-07	10
artery smooth muscle tissue	2.61e-07	10
aorta smooth muscle tissue	2.61e-07	10
organ component layer	5.09e-07	57
immaterial anatomical entity	6.14e-07	126
skin of body	8.12e-07	40

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
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379997651546202
PRDM1#639	2	43.9436519258203	0.000845206071603017	0.00637254381404472

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.