Coexpression cluster:C3347

Full id: C3347_Endothelial_acute_Hepatic_Renal_Lymphatic_large_CD14

Phase1 CAGE Peaks

Hg19::chr12:96588368..96588394,+	p3@ELK3
Hg19::chrX:71299606..71299619,+	p@chrX:71299606..71299619 +
Hg19::chrX:71299620..71299649,+	p@chrX:71299620..71299649 +

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	7.99e-29	36
endothelial cell of vascular tree	9.37e-29	24
blood vessel endothelial cell	4.45e-22	18
embryonic blood vessel endothelial progenitor cell	4.45e-22	18
meso-epithelial cell	1.85e-20	45
classical monocyte	1.49e-14	42
CD14-positive, CD16-negative classical monocyte	1.49e-14	42
lining cell	3.43e-13	58
barrier cell	3.43e-13	58
defensive cell	3.97e-13	48
phagocyte	3.97e-13	48
endothelial cell of artery	7.11e-12	9
myeloid leukocyte	1.02e-09	72
myeloid cell	1.41e-09	108
common myeloid progenitor	1.41e-09	108
myeloid lineage restricted progenitor cell	2.18e-09	66
monopoietic cell	2.59e-09	59
monocyte	2.59e-09	59
monoblast	2.59e-09	59
promonocyte	2.59e-09	59
granulocyte monocyte progenitor cell	4.21e-09	67
macrophage dendritic cell progenitor	1.03e-08	61
vein endothelial cell	1.31e-08	6
aortic endothelial cell	1.74e-08	6
lymphangioblast	3.24e-08	6
endothelial cell of lymphatic vessel	3.24e-08	6
vascular lymphangioblast	3.24e-08	6

Uber Anatomy

Ontology term	p-value	n
blood vessel endothelium	4.45e-22	18
endothelium	4.45e-22	18
cardiovascular system endothelium	4.45e-22	18
lateral plate mesoderm	3.03e-18	203
simple squamous epithelium	1.07e-16	22
adult organism	2.50e-15	114
vessel	5.83e-14	68
squamous epithelium	7.90e-14	25
vasculature	1.18e-12	78
vascular system	1.18e-12	78
circulatory system	1.48e-12	112
immune system	3.44e-12	93
mesoderm	5.18e-12	315
mesoderm-derived structure	5.18e-12	315
presumptive mesoderm	5.18e-12	315
endothelial tube	7.11e-12	9
arterial system endothelium	7.11e-12	9
endothelium of artery	7.11e-12	9
splanchnic layer of lateral plate mesoderm	2.07e-11	83
cardiovascular system	2.80e-11	109
epithelial tube open at both ends	9.47e-11	59
blood vessel	9.47e-11	59
blood vasculature	9.47e-11	59
vascular cord	9.47e-11	59
hemolymphoid system	2.78e-10	108
epithelial tube	6.64e-08	117
bone marrow	1.71e-07	76
hematopoietic system	6.23e-07	98
blood island	6.23e-07	98
lymphoid system	6.93e-07	10
vein	8.88e-07	9
venous blood vessel	8.88e-07	9
venous system	8.88e-07	9
anatomical conduit	9.40e-07	240

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
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895778349656121
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.032896021248661

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.