MCL coexpression mm9:416

Phase1 CAGE Peaks

	Short description
Mm9::chr10:5734717..5734727,-	p12@Esr1
Mm9::chr10:75399907..75399919,+	p@chr10:75399907..75399919 +
Mm9::chr12:16596549..16596632,-	p1@Lpin1
Mm9::chr12:72977020..72977051,+	p@chr12:72977020..72977051 +
Mm9::chr15:76137124..76137135,-	p@chr15:76137124..76137135 -
Mm9::chr18:64639050..64639061,-	p@chr18:64639050..64639061 -
Mm9::chr3:129234914..129234917,-	p@chr3:129234914..129234917 -
Mm9::chr4:147976089..147976106,+	p@chr4:147976089..147976106 +
Mm9::chr5:125976345..125976366,+	p@chr5:125976345..125976366 +
Mm9::chr5:66473042..66473055,-	p@chr5:66473042..66473055 -
Mm9::chr6:142421318..142421325,-	p8@Gys2
Mm9::chr6:142421333..142421360,-	p5@Gys2
Mm9::chr6:142421364..142421402,-	p2@Gys2
Mm9::chr6:142421417..142421436,-	p4@Gys2
Mm9::chr6:142421480..142421505,-	p3@Gys2
Mm9::chr7:148021087..148021088,+	p7@1190003J15Rik
Mm9::chr8:113560785..113560799,+	p@chr8:113560785..113560799 +
Mm9::chr9:106150191..106150205,-	p1@Alas1

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:0031529	ruffle organization and biogenesis	0.0124236528193307
GO:0019842	vitamin binding	0.0124236528193307
GO:0032868	response to insulin stimulus	0.0124236528193307
GO:0043434	response to peptide hormone stimulus	0.0124236528193307
GO:0032870	cellular response to hormone stimulus	0.0124236528193307
GO:0045839	negative regulation of mitosis	0.0124236528193307
GO:0016749	N-succinyltransferase activity	0.0124236528193307
GO:0004373	glycogen (starch) synthase activity	0.0124236528193307
GO:0032869	cellular response to insulin stimulus	0.0124236528193307
GO:0003870	5-aminolevulinate synthase activity	0.0124236528193307
GO:0031532	actin cytoskeleton reorganization	0.0133092333762021
GO:0016748	succinyltransferase activity	0.0133092333762021
GO:0004813	alanine-tRNA ligase activity	0.0133092333762021
GO:0006419	alanyl-tRNA aminoacylation	0.0133092333762021
GO:0006590	thyroid hormone generation	0.0206975809343111
GO:0035251	UDP-glucosyltransferase activity	0.0219120840674093
GO:0008195	phosphatidate phosphatase activity	0.0219120840674093
GO:0046527	glucosyltransferase activity	0.0241405635418043
GO:0019841	retinol binding	0.0248268930780587
GO:0045598	regulation of fat cell differentiation	0.0248268930780587
GO:0042403	thyroid hormone metabolic process	0.0260103751302593
GO:0016918	retinal binding	0.0260103751302593
GO:0006519	amino acid and derivative metabolic process	0.0260103751302593
GO:0009250	glucan biosynthetic process	0.0260103751302593
GO:0005978	glycogen biosynthetic process	0.0260103751302593
GO:0006783	heme biosynthetic process	0.0260103751302593
GO:0009058	biosynthetic process	0.0260103751302593
GO:0033014	tetrapyrrole biosynthetic process	0.0260103751302593
GO:0006779	porphyrin biosynthetic process	0.0260103751302593
GO:0005501	retinoid binding	0.0260103751302593
GO:0019840	isoprenoid binding	0.0260103751302593
GO:0009308	amine metabolic process	0.0271903979283695
GO:0009725	response to hormone stimulus	0.0286942308675125
GO:0042168	heme metabolic process	0.0286942308675125
GO:0006807	nitrogen compound metabolic process	0.0286942308675125
GO:0033692	cellular polysaccharide biosynthetic process	0.0293600272437102
GO:0033013	tetrapyrrole metabolic process	0.0293600272437102
GO:0006778	porphyrin metabolic process	0.0293600272437102
GO:0000271	polysaccharide biosynthetic process	0.0301923598486603
GO:0051716	cellular response to stimulus	0.0309826520203106
GO:0045444	fat cell differentiation	0.0347467450100203
GO:0046148	pigment biosynthetic process	0.0373293804433897
GO:0007088	regulation of mitosis	0.0373293804433897
GO:0000902	cell morphogenesis	0.0373293804433897
GO:0032989	cellular structure morphogenesis	0.0373293804433897
GO:0006073	glucan metabolic process	0.0399590170377478
GO:0005977	glycogen metabolic process	0.0399590170377478
GO:0042440	pigment metabolic process	0.0399590170377478
GO:0016769	transferase activity, transferring nitrogenous groups	0.0432867010868868
GO:0006112	energy reserve metabolic process	0.0432867010868868
GO:0019748	secondary metabolic process	0.0480042215885874
GO:0006418	tRNA aminoacylation for protein translation	0.0480042215885874
GO:0043038	amino acid activation	0.0480042215885874
GO:0043039	tRNA aminoacylation	0.0480042215885874
GO:0030170	pyridoxal phosphate binding	0.0480042215885874
GO:0005976	polysaccharide metabolic process	0.0480042215885874
GO:0005496	steroid binding	0.0480042215885874
GO:0003707	steroid hormone receptor activity	0.0480042215885874
GO:0044264	cellular polysaccharide metabolic process	0.0480042215885874
GO:0004879	ligand-dependent nuclear receptor activity	0.0480042215885874
GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	0.0480042215885874
GO:0016875	ligase activity, forming carbon-oxygen bonds	0.0480042215885874
GO:0004812	aminoacyl-tRNA ligase activity	0.0480042215885874
GO:0009059	macromolecule biosynthetic process	0.0495027323876971

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
metabolising cell	1.72e-07	5
endopolyploid cell	1.72e-07	5
parenchymal cell	1.72e-07	5
polyploid cell	1.72e-07	5
hepatocyte	1.72e-07	5

Uber Anatomy

Ontology term	p-value	n
exocrine gland	1.99e-28	25
exocrine system	1.99e-28	25
liver	4.08e-27	22
epithelial sac	4.08e-27	22
digestive gland	4.08e-27	22
epithelium of foregut-midgut junction	4.08e-27	22
anatomical boundary	4.08e-27	22
hepatobiliary system	4.08e-27	22
foregut-midgut junction	4.08e-27	22
hepatic diverticulum	4.08e-27	22
liver primordium	4.08e-27	22
septum transversum	4.08e-27	22
liver bud	4.08e-27	22
digestive tract diverticulum	1.04e-25	23
sac	1.04e-25	23
abdomen element	8.34e-18	49
abdominal segment element	8.34e-18	49
abdominal segment of trunk	8.34e-18	49
abdomen	8.34e-18	49
trunk mesenchyme	5.57e-15	45
mesenchyme	5.02e-13	61
entire embryonic mesenchyme	5.02e-13	61
epithelial tube	7.89e-13	47
subdivision of trunk	1.47e-11	66
gland	1.22e-10	65
endocrine gland	7.89e-10	60
trunk region element	1.22e-08	79
gut epithelium	6.78e-08	55
endocrine system	2.66e-07	72
trunk	7.36e-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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