Coexpression cluster:C4394

Full id: C4394_neuroblastoma_Mesenchymal_rectum_heart_neuroectodermal_leiomyoma_gall

Phase1 CAGE Peaks

Hg19::chr4:174451350..174451363,-	p3@HAND2
Hg19::chr4:174451370..174451387,-	p1@HAND2
Hg19::chr4:174451596..174451632,+	p1@NBLA00301

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:0007507	heart development	0.038276619961537
GO:0001525	angiogenesis	0.038276619961537
GO:0048514	blood vessel morphogenesis	0.038276619961537
GO:0048646	anatomical structure formation	0.038276619961537
GO:0001568	blood vessel development	0.038276619961537
GO:0001944	vasculature development	0.038276619961537

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
muscle cell	3.34e-11	55
smooth muscle cell	6.65e-11	43
smooth muscle myoblast	6.65e-11	43
muscle precursor cell	1.57e-10	58
myoblast	1.57e-10	58
multi-potent skeletal muscle stem cell	1.57e-10	58
extraembryonic cell	6.20e-10	19
contractile cell	1.39e-09	59
electrically responsive cell	2.31e-09	61
electrically active cell	2.31e-09	61
vascular associated smooth muscle cell	3.41e-08	32
fibroblast	3.73e-08	76
cardiocyte	1.91e-07	16

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	1.32e-16	83
primary circulatory organ	8.45e-16	27
heart	3.28e-13	24
primitive heart tube	3.28e-13	24
primary heart field	3.28e-13	24
anterior lateral plate mesoderm	3.28e-13	24
heart tube	3.28e-13	24
heart primordium	3.28e-13	24
cardiac mesoderm	3.28e-13	24
cardiogenic plate	3.28e-13	24
heart rudiment	3.28e-13	24
extraembryonic structure	1.52e-12	24
muscle tissue	2.85e-11	64
musculature	2.85e-11	64
musculature of body	2.85e-11	64
epithelial tube	2.54e-10	117
skeletal muscle tissue	3.67e-10	62
striated muscle tissue	3.67e-10	62
myotome	3.67e-10	62
somite	5.90e-10	71
presomitic mesoderm	5.90e-10	71
presumptive segmental plate	5.90e-10	71
dermomyotome	5.90e-10	71
trunk paraxial mesoderm	5.90e-10	71
mesoderm	6.14e-10	315
mesoderm-derived structure	6.14e-10	315
presumptive mesoderm	6.14e-10	315
circulatory system	6.96e-10	112
paraxial mesoderm	1.27e-09	72
presumptive paraxial mesoderm	1.27e-09	72
extraembryonic membrane	1.95e-09	14
membranous layer	1.95e-09	14
artery	2.08e-09	42
arterial blood vessel	2.08e-09	42
arterial system	2.08e-09	42
dense mesenchyme tissue	2.66e-09	73
multi-cellular organism	3.36e-09	656
mesenchyme	7.15e-09	160
entire embryonic mesenchyme	7.15e-09	160
epithelial tube open at both ends	8.08e-09	59
blood vessel	8.08e-09	59
blood vasculature	8.08e-09	59
vascular cord	8.08e-09	59
cardiovascular system	1.76e-08	109
trunk mesenchyme	2.40e-08	122
epithelial vesicle	7.49e-08	78
multilaminar epithelium	1.39e-07	83
systemic artery	6.99e-07	33
systemic arterial system	6.99e-07	33
vessel	9.22e-07	68
organ component layer	9.51e-07	66

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
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168059518058296
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330614698283624

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.