Coexpression cluster:C4078

Full id: C4078_Mast_Endothelial_Lymphatic_Melanocyte_melanoma_Hep2_Hepatic

Phase1 CAGE Peaks

Hg19::chr21:42540033..42540062,+	p2@BACE2
Hg19::chr21:42540070..42540107,+	p1@BACE2
Hg19::chr21:42540108..42540124,+	p3@BACE2

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
epithelial cell	6.99e-21	254
mesodermal cell	3.43e-16	119
embryonic cell	3.67e-15	248
endothelial cell of vascular tree	3.42e-14	24
lining cell	7.28e-13	57
barrier cell	7.28e-13	57
endothelial cell	1.87e-12	35
meso-epithelial cell	1.97e-12	44
blood vessel endothelial cell	3.41e-10	18
embryonic blood vessel endothelial progenitor cell	3.41e-10	18
squamous epithelial cell	1.37e-09	62
non-terminally differentiated cell	1.93e-07	180

Uber Anatomy

Ontology term	p-value	n
vasculature	1.08e-17	79
vascular system	1.08e-17	79
vessel	1.55e-17	69
splanchnic layer of lateral plate mesoderm	8.43e-16	84
epithelial tube	1.14e-15	118
blood vessel	2.02e-15	60
epithelial tube open at both ends	2.02e-15	60
blood vasculature	2.02e-15	60
vascular cord	2.02e-15	60
anatomical cluster	9.31e-14	286
cardiovascular system	4.98e-13	110
circulatory system	1.36e-12	113
cell layer	1.77e-12	312
epithelium	1.85e-12	309
anatomical conduit	1.67e-10	241
artery	1.88e-10	42
arterial blood vessel	1.88e-10	42
arterial system	1.88e-10	42
endothelium	3.41e-10	18
blood vessel endothelium	3.41e-10	18
cardiovascular system endothelium	3.41e-10	18
mesenchyme	4.69e-10	238
entire embryonic mesenchyme	4.69e-10	238
multi-tissue structure	1.32e-09	347
systemic artery	1.53e-09	33
systemic arterial system	1.53e-09	33
multi-cellular organism	3.90e-09	659
primordium	1.00e-08	168
compound organ	1.10e-08	69
simple squamous epithelium	2.16e-08	22
unilaminar epithelium	3.50e-08	138
squamous epithelium	5.22e-08	25
trunk	8.01e-08	216
organ segment	1.46e-07	97
anatomical system	2.21e-07	625
larynx	2.60e-07	9
anatomical group	3.80e-07	626
organ part	4.26e-07	219
tube	4.70e-07	194
organism subdivision	9.58e-07	365

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115398288390486
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279974884945594
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172016584914066
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325964384034946
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000852469350668577
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140479631042936
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109601789968019

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.