MCL coexpression mm9:3349

Phase1 CAGE Peaks

	Short description
Mm9::chr2:38142694..38142715,-	p2@Dennd1a
Mm9::chr2:38142729..38142745,-	p3@Dennd1a
Mm9::chr3:135148569..135148632,+	p1@Manba

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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GO ID	GO name	FDR corrected p-value
GO:0004567	beta-mannosidase activity	0.00690297485344875
GO:0048488	synaptic vesicle endocytosis	0.0172508185679887
GO:0006516	glycoprotein catabolic process	0.0172508185679887
GO:0017124	SH3 domain binding	0.0172508185679887
GO:0015923	mannosidase activity	0.0172508185679887
GO:0030665	clathrin coated vesicle membrane	0.0172508185679887
GO:0048489	synaptic vesicle transport	0.0224193037463458
GO:0030662	coated vesicle membrane	0.0224193037463458
GO:0030659	cytoplasmic vesicle membrane	0.0280618538186314
GO:0030425	dendrite	0.0280618538186314
GO:0044433	cytoplasmic vesicle part	0.0280618538186314
GO:0019904	protein domain specific binding	0.0280618538186314
GO:0012506	vesicle membrane	0.0280618538186314
GO:0043025	cell soma	0.0280618538186314
GO:0030136	clathrin-coated vesicle	0.0339865740550138
GO:0030135	coated vesicle	0.0352437618835035
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0352437618835035
GO:0009100	glycoprotein metabolic process	0.0374829962895571
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0391229485738048
GO:0043005	neuron projection	0.0399111231992233
GO:0010324	membrane invagination	0.0486697011754536
GO:0006897	endocytosis	0.0486697011754536
GO:0005764	lysosome	0.0486697011754536
GO:0000323	lytic vacuole	0.0486697011754536
GO:0016023	cytoplasmic membrane-bound vesicle	0.0493369173761718
GO:0005773	vacuole	0.0493369173761718
GO:0031988	membrane-bound vesicle	0.0493369173761718

Relative expression of the co-expression cluster over median <br>Analyst:

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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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	3.98e-09	118
endoderm	3.98e-09	118
presumptive endoderm	3.98e-09	118
digestive tract diverticulum	9.04e-09	23
sac	9.04e-09	23
trunk region element	1.14e-08	79
subdivision of digestive tract	1.23e-08	114
liver	1.39e-08	22
epithelial sac	1.39e-08	22
digestive gland	1.39e-08	22
epithelium of foregut-midgut junction	1.39e-08	22
anatomical boundary	1.39e-08	22
hepatobiliary system	1.39e-08	22
foregut-midgut junction	1.39e-08	22
hepatic diverticulum	1.39e-08	22
liver primordium	1.39e-08	22
septum transversum	1.39e-08	22
liver bud	1.39e-08	22
endo-epithelium	1.43e-08	69
digestive system	2.51e-08	116
digestive tract	2.51e-08	116
primitive gut	2.51e-08	116
exocrine gland	4.44e-08	25
exocrine system	4.44e-08	25
subdivision of trunk	1.48e-07	66
foregut	1.53e-07	80
abdomen element	2.57e-07	49
abdominal segment element	2.57e-07	49
abdominal segment of trunk	2.57e-07	49
abdomen	2.57e-07	49
trunk	4.02e-07	90

TFBS overrepresentation<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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