Coexpression cluster:C330

Full id: C330_bronchioalveolar_oral_signet_embryonic_lymphangiectasia_testis_adult

Phase1 CAGE Peaks

Hg19::chr11:106266838..106266843,+	p@chr11:106266838..106266843 +
Hg19::chr11:15583363..15583369,+	p@chr11:15583363..15583369 +
Hg19::chr11:41809203..41809208,-	p@chr11:41809203..41809208 -
Hg19::chr11:69002103..69002105,-	p@chr11:69002103..69002105 -
Hg19::chr11:69002371..69002382,-	p@chr11:69002371..69002382 -
Hg19::chr11:69002385..69002407,-	p@chr11:69002385..69002407 -
Hg19::chr12:47628787..47628808,+	p10@FAM113B
Hg19::chr13:111618030..111618074,+	p@chr13:111618030..111618074 +
Hg19::chr13:111629545..111629550,+	p@chr13:111629545..111629550 +
Hg19::chr13:70823810..70823813,+	p@chr13:70823810..70823813 +
Hg19::chr14:36536932..36536937,-	p@chr14:36536932..36536937 -
Hg19::chr14:74034310..74034345,+	p4@ACOT2
Hg19::chr14:88200641..88200643,-	p1@ENST00000556168
Hg19::chr15:40366561..40366568,-	p@chr15:40366561..40366568 -
Hg19::chr15:75356166..75356171,+	p@chr15:75356166..75356171 +
Hg19::chr17:66077866..66077872,+	p@chr17:66077866..66077872 +
Hg19::chr1:166958538..166958552,+	p2@MAEL
Hg19::chr1:166964233..166964235,+	p@chr1:166964233..166964235 +
Hg19::chr1:87994589..87994604,-	p@chr1:87994589..87994604 -
Hg19::chr20:26116667..26116670,+	p@chr20:26116667..26116670 +
Hg19::chr3:87647430..87647437,-	p@chr3:87647430..87647437 -
Hg19::chr4:169956294..169956301,-	p@chr4:169956294..169956301 -
Hg19::chr4:171012844..171012850,-	p12@AADAT
Hg19::chr4:42315859..42315864,+	p@chr4:42315859..42315864 +
Hg19::chr7:16955191..16955205,+	p@chr7:16955191..16955205 +
Hg19::chr7:16955957..16955989,+	p@chr7:16955957..16955989 +
Hg19::chr7:4833949..4833955,+	p@chr7:4833949..4833955 +
Hg19::chr7:5834097..5834103,+	p@chr7:5834097..5834103 +
Hg19::chr8:122157279..122157284,-	p@chr8:122157279..122157284 -
Hg19::chr8:144260966..144260967,-	p@chr8:144260966..144260967 -
Hg19::chr8:15364131..15364145,-	p@chr8:15364131..15364145 -
Hg19::chr9:103785643..103785646,-	p@chr9:103785643..103785646 -
Hg19::chr9:79057008..79057019,+	p5@GCNT1
Hg19::chr9:87024410..87024417,+	p@chr9:87024410..87024417 +
Hg19::chrX:48056224..48056233,-	p1@SSX5

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:0047536	2-aminoadipate transaminase activity	0.0128024012211761
GO:0003829	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity	0.0128024012211761
GO:0016212	kynurenine-oxoglutarate transaminase activity	0.0128024012211761
GO:0001676	long-chain fatty acid metabolic process	0.0128024012211761
GO:0016290	palmitoyl-CoA hydrolase activity	0.0191979495576364
GO:0000038	very-long-chain fatty acid metabolic process	0.0191979495576364
GO:0006637	acyl-CoA metabolic process	0.0292419644481353
GO:0016291	acyl-CoA thioesterase activity	0.0335726840533861
GO:0016289	CoA hydrolase activity	0.0369368408147647
GO:0006493	protein amino acid O-linked glycosylation	0.0383484563431187
GO:0008375	acetylglucosaminyltransferase activity	0.0489546679572067
GO:0008483	transaminase activity	0.0489546679572067

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
pneumocyte	1.22e-14	3

Uber Anatomy

Ontology term	p-value	n
bronchoalveolar duct junction	3.11e-21	2
alveolar duct	3.11e-21	2
bronchiole	3.11e-21	2
testis	8.12e-21	8
male reproductive organ	1.88e-15	11
pulmonary alveolus epithelium	1.22e-14	3
alveolus	1.22e-14	3
pulmonary lobule	1.22e-14	3
lobule	1.22e-14	3
alveolus of lung	1.22e-14	3
alveolar system	1.22e-14	3
pulmonary acinus	1.22e-14	3
alveolar sac	1.22e-14	3
alveolar wall	1.22e-14	3
gonad	1.37e-08	21
indifferent external genitalia	1.37e-08	21
indifferent gonad	1.37e-08	21
gonad primordium	1.37e-08	21
external genitalia	3.04e-08	22
male organism	3.04e-08	22
male reproductive system	3.04e-08	22

Disease

Ontology term	p-value	n
lung adenocarcinoma	3.11e-21	2
non-small cell lung carcinoma	2.53e-09	5
bronchus cancer	5.08e-07	7
bronchogenic carcinoma	5.08e-07	7

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
NFYA#4800	14	7.37023227993221	1.49137435499956e-09	1.32446978113775e-07
NFYB#4801	12	5.74621482978393	4.62112102364577e-07	2.18778449042856e-05

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.