Coexpression cluster:C557

Full id: C557_Lymphatic_Endothelial_mesothelioma_pleomorphic_Cardiac_lung_aorta

Phase1 CAGE Peaks

Hg19::chr11:108794408..108794422,+	p@chr11:108794408..108794422 +
Hg19::chr11:108794429..108794441,+	p@chr11:108794429..108794441 +
Hg19::chr11:108794468..108794473,+	p@chr11:108794468..108794473 +
Hg19::chr12:46807404..46807413,+	p@chr12:46807404..46807413 +
Hg19::chr1:66723029..66723041,+	p54@PDE4B
Hg19::chr2:170930109..170930110,+	p3@AL833423
Hg19::chr3:145968814..145968846,-	p2@PLSCR4
Hg19::chr4:114238302..114238314,+	p67@ANK2
Hg19::chr6:84849274..84849294,+	p@chr6:84849274..84849294 +
Hg19::chr7:79998842..79998855,+	p25@CD36
Hg19::chr7:79998864..79998896,+	p12@CD36
Hg19::chr7:79998905..79998917,+	p26@CD36
Hg19::chr7:79998932..79998956,+	p17@CD36
Hg19::chr7:79999026..79999038,+	p31@CD36
Hg19::chr9:13446440..13446456,+	p2@ENST00000428006
Hg19::chr9:13446472..13446510,+	p1@ENST00000428006

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:0007596	blood coagulation	0.00126852059183336
GO:0050817	coagulation	0.00126852059183336
GO:0007599	hemostasis	0.00126852059183336
GO:0050878	regulation of body fluid levels	0.00126852059183336
GO:0042060	wound healing	0.00126852059183336
GO:0017128	phospholipid scramblase activity	0.00484368389615771
GO:0017121	phospholipid scrambling	0.00484368389615771
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.00730233978810365
GO:0009611	response to wounding	0.00730233978810365
GO:0007009	plasma membrane organization and biogenesis	0.0110150024093571
GO:0009605	response to external stimulus	0.0132790655320293
GO:0005626	insoluble fraction	0.0141174333515346
GO:0005548	phospholipid transporter activity	0.0208393166100831
GO:0000267	cell fraction	0.0209698967234201
GO:0065008	regulation of biological quality	0.0218046051086361
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0233904230898605
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0233904230898605
GO:0006950	response to stress	0.0295632196082685
GO:0005200	structural constituent of cytoskeleton	0.0377855298244911
GO:0005319	lipid transporter activity	0.0405219551907834

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
capillary endothelial cell	2.09e-27	3
lymphangioblast	2.39e-24	6
endothelial cell of lymphatic vessel	2.39e-24	6
vascular lymphangioblast	2.39e-24	6
endothelial cell of vascular tree	1.30e-17	24
endothelial cell	1.72e-11	36
meso-epithelial cell	4.90e-09	45
lining cell	7.83e-07	58
barrier cell	7.83e-07	58

Uber Anatomy

Ontology term	p-value	n
lymphoid system	1.60e-31	10
microcirculatory vessel	2.09e-27	3
endothelium of capillary	2.09e-27	3
capillary	2.09e-27	3
lymphatic vessel	2.50e-18	8
lymph vasculature	2.50e-18	8
lymphatic part of lymphoid system	2.50e-18	8
open tracheal system trachea	4.48e-18	2
lymph node	2.84e-10	1
tonsil	1.17e-09	1
mucosa-associated lymphoid tissue	1.17e-09	1
lymphoid tissue	1.17e-09	1
tonsillar ring	1.17e-09	1
thyroid gland	6.77e-08	5
pharyngeal pouch	6.77e-08	5
thyroid diverticulum	6.77e-08	5
pharyngeal pouch 2	6.77e-08	5
thyroid primordium	6.77e-08	5
small intestine	8.32e-08	4
vessel	2.22e-07	68

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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No analysis results for this cluster

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.