Coexpression cluster:C296

Full id: C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed

Phase1 CAGE Peaks

Hg19::chr10:103952998..103953003,-	p@chr10:103952998..103953003 -
Hg19::chr10:124050589..124050596,+	p15@BTBD16
Hg19::chr10:73818867..73818877,-	p@chr10:73818867..73818877 -
Hg19::chr11:63331619..63331629,-	p7@AK025029
Hg19::chr11:86501675..86501685,+	p29@PRSS23
Hg19::chr11:86501763..86501768,+	p33@PRSS23
Hg19::chr14:68633950..68633964,-	p@chr14:68633950..68633964 -
Hg19::chr14:94582961..94582978,+	p@chr14:94582961..94582978 +
Hg19::chr17:5813133..5813142,-	p@chr17:5813133..5813142 -
Hg19::chr1:27992626..27992630,-	p@chr1:27992626..27992630 -
Hg19::chr1:27992654..27992665,-	p@chr1:27992654..27992665 -
Hg19::chr1:27992698..27992702,-	p@chr1:27992698..27992702 -
Hg19::chr1:27992756..27992763,-	p@chr1:27992756..27992763 -
Hg19::chr1:27992774..27992780,-	p@chr1:27992774..27992780 -
Hg19::chr1:79107935..79107976,+	p@chr1:79107935..79107976 +
Hg19::chr1:94583454..94583465,-	p@chr1:94583454..94583465 -
Hg19::chr20:4100484..4100497,+	p1@BC027448
Hg19::chr20:4100520..4100530,+	p2@BC027448
Hg19::chr20:4100562..4100570,+	p4@BC027448
Hg19::chr20:4100596..4100603,+	p5@BC027448
Hg19::chr21:42613665..42613680,+	p10@BACE2
Hg19::chr22:31985409..31985436,+	p@chr22:31985409..31985436 +
Hg19::chr22:31985448..31985465,+	p@chr22:31985448..31985465 +
Hg19::chr22:50983547..50983560,-	p@chr22:50983547..50983560 -
Hg19::chr2:121003683..121003689,-	p@chr2:121003683..121003689 -
Hg19::chr2:42157172..42157179,-	p@chr2:42157172..42157179 -
Hg19::chr2:42157397..42157411,-	p@chr2:42157397..42157411 -
Hg19::chr3:186648149..186648166,+	p12@ST6GAL1
Hg19::chr3:195516631..195516648,-	p@chr3:195516631..195516648 -
Hg19::chr3:195516657..195516687,-	p@chr3:195516657..195516687 -
Hg19::chr3:23688310..23688316,+	p@chr3:23688310..23688316 +
Hg19::chr4:6698835..6698866,+	p@chr4:6698835..6698866 +
Hg19::chr5:147644551..147644576,+	p@chr5:147644551..147644576 +
Hg19::chr5:147645292..147645302,+	p@chr5:147645292..147645302 +
Hg19::chr5:84867331..84867340,-	p@chr5:84867331..84867340 -
Hg19::chr5:84943630..84943645,-	p@chr5:84943630..84943645 -
Hg19::chr9:95736745..95736757,+	p9@FGD3
Hg19::chr9:95736758..95736771,+	p7@FGD3
Hg19::chr9:95736796..95736808,+	p11@FGD3
Hg19::chr9:95736917..95736936,+	p10@FGD3
Hg19::chr9:95737369..95737393,+	p18@FGD3
Hg19::chr9:95737958..95737978,+	p@chr9:95737958..95737978 +

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:0009101	glycoprotein biosynthetic process	0.0153040198506013
GO:0009100	glycoprotein metabolic process	0.0153040198506013
GO:0042985	negative regulation of amyloid precursor protein biosynthetic process	0.0153040198506013
GO:0042983	amyloid precursor protein biosynthetic process	0.0153040198506013
GO:0003835	beta-galactoside alpha-2,6-sialyltransferase activity	0.0153040198506013
GO:0042984	regulation of amyloid precursor protein biosynthetic process	0.0153040198506013
GO:0009049	aspartic-type signal peptidase activity	0.0163961987631881
GO:0016486	peptide hormone processing	0.0187766779372494
GO:0032488	Cdc42 protein signal transduction	0.0187766779372494
GO:0043088	regulation of Cdc42 GTPase activity	0.0187766779372494
GO:0032489	regulation of Cdc42 protein signal transduction	0.0187766779372494
GO:0032319	regulation of Rho GTPase activity	0.0198846865302194
GO:0033619	membrane protein proteolysis	0.0198846865302194
GO:0009003	signal peptidase activity	0.0198846865302194
GO:0006509	membrane protein ectodomain proteolysis	0.0198846865302194
GO:0042982	amyloid precursor protein metabolic process	0.0200747034966908
GO:0050435	beta-amyloid metabolic process	0.0229384663849809
GO:0009311	oligosaccharide metabolic process	0.0275148176906598
GO:0046847	filopodium formation	0.0275148176906598
GO:0030035	microspike biogenesis	0.0275148176906598
GO:0004194	pepsin A activity	0.0283849614143019
GO:0005794	Golgi apparatus	0.0284450184777538
GO:0004175	endopeptidase activity	0.0339601840165598
GO:0008373	sialyltransferase activity	0.0339601840165598
GO:0030027	lamellipodium	0.0339601840165598
GO:0022603	regulation of anatomical structure morphogenesis	0.0339601840165598
GO:0022604	regulation of cell morphogenesis	0.0339601840165598
GO:0008360	regulation of cell shape	0.0339601840165598
GO:0001726	ruffle	0.0339601840165598
GO:0030031	cell projection biogenesis	0.0381565712327612
GO:0009306	protein secretion	0.0420779689934136
GO:0030173	integral to Golgi membrane	0.0436133239286936
GO:0031228	intrinsic to Golgi membrane	0.0484185353590127
GO:0031252	leading edge	0.0484185353590127
GO:0006959	humoral immune response	0.0489862934759819

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.94e-07	254

Uber Anatomy

Ontology term	p-value	n
adult organism	9.62e-12	115
digestive system	6.00e-09	155
digestive tract	6.00e-09	155
primitive gut	6.00e-09	155
subdivision of digestive tract	8.77e-09	129
endodermal part of digestive tract	8.77e-09	129
organ	9.64e-09	511
endoderm-derived structure	1.34e-08	169
endoderm	1.34e-08	169
presumptive endoderm	1.34e-08	169

Disease

Ontology term	p-value	n
carcinoma	3.35e-21	106
cell type cancer	3.73e-16	143
cancer	5.71e-10	235
disease of cellular proliferation	4.73e-09	239

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)
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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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