Coexpression cluster:C3346

Full id: C3346_Endothelial_Renal_somatostatinoma_Lymphatic_Small_Fibroblast_Natural

Phase1 CAGE Peaks

Hg19::chr12:96028776..96028781,-	p@chr12:96028776..96028781 -
Hg19::chr5:106837869..106837878,-	p@chr5:106837869..106837878 -
Hg19::chr5:106837881..106837888,-	p@chr5:106837881..106837888 -

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
endothelial cell of vascular tree	5.44e-50	24
endothelial cell	2.09e-39	35
blood vessel endothelial cell	5.07e-34	18
embryonic blood vessel endothelial progenitor cell	5.07e-34	18
meso-epithelial cell	6.83e-33	44
lining cell	1.50e-23	57
barrier cell	1.50e-23	57
lymphangioblast	8.41e-18	6
endothelial cell of lymphatic vessel	8.41e-18	6
vascular lymphangioblast	8.41e-18	6
endothelial cell of artery	2.29e-15	9
vein endothelial cell	3.50e-12	6
capillary endothelial cell	3.22e-10	3
mesodermal cell	8.32e-10	119
endothelial cell of umbilical vein	1.50e-09	3
squamous epithelial cell	2.58e-09	62
epithelial cell	5.87e-09	254
aortic endothelial cell	3.53e-08	6
thoracic aorta endothelial cell	9.61e-07	2

Uber Anatomy

Ontology term	p-value	n
endothelium	5.07e-34	18
blood vessel endothelium	5.07e-34	18
cardiovascular system endothelium	5.07e-34	18
simple squamous epithelium	9.03e-31	22
squamous epithelium	1.54e-26	25
vessel	4.50e-18	69
vasculature	2.54e-16	79
vascular system	2.54e-16	79
endothelial tube	2.29e-15	9
arterial system endothelium	2.29e-15	9
endothelium of artery	2.29e-15	9
lymphatic vessel	3.85e-13	8
lymph vasculature	3.85e-13	8
lymphatic part of lymphoid system	3.85e-13	8
blood vessel	4.02e-11	60
epithelial tube open at both ends	4.02e-11	60
blood vasculature	4.02e-11	60
vascular cord	4.02e-11	60
epithelial tube	1.71e-10	118
anatomical conduit	2.11e-10	241
lymphoid system	2.42e-10	10
endothelium of capillary	3.22e-10	3
capillary	3.22e-10	3
cardiovascular system	7.19e-10	110
anatomical cluster	1.38e-09	286
circulatory system	1.93e-09	113
pharynx	5.14e-08	11
vein	5.66e-08	9
venous blood vessel	5.66e-08	9
venous system	5.66e-08	9
segment of aorta	9.61e-07	2
thoracic aorta	9.61e-07	2

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	0.0167098270441828
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895722374004703
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00436324432446103
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443488941659458

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.