MCL coexpression mm9:810

Phase1 CAGE Peaks

	Short description
Mm9::chr12:85379338..85379385,+	p1@Acot4
Mm9::chr18:61879449..61879487,-	p@chr18:61879449..61879487 -
Mm9::chr19:10678794..10678805,-	p4@Dak
Mm9::chr2:155418444..155418506,-	p1@Gss
Mm9::chr2:163367451..163367464,-	p1@0610008F07Rik
Mm9::chr2:163372869..163372882,+	p3@Hnf4a
Mm9::chr2:163372884..163372904,+	p1@Hnf4a
Mm9::chr3:94176733..94176794,+	p1@Rorc
Mm9::chr6:43616157..43616223,-	p1@Tpk1

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:0006732	coenzyme metabolic process	0.00158271079552393
GO:0051186	cofactor metabolic process	0.00158271079552393
GO:0003707	steroid hormone receptor activity	0.00385919243044701
GO:0004879	ligand-dependent nuclear receptor activity	0.00385919243044701
GO:0009108	coenzyme biosynthetic process	0.00457210022760891
GO:0042357	thiamin diphosphate metabolic process	0.00457210022760891
GO:0004363	glutathione synthase activity	0.00457210022760891
GO:0009229	thiamin diphosphate biosynthetic process	0.00457210022760891
GO:0004371	glycerone kinase activity	0.00457210022760891
GO:0042724	thiamin and derivative biosynthetic process	0.00457210022760891
GO:0004788	thiamin diphosphokinase activity	0.00457210022760891
GO:0051188	cofactor biosynthetic process	0.00516392620901728
GO:0006772	thiamin metabolic process	0.00670482850567052
GO:0048537	mucosal-associated lymphoid tissue development	0.00670482850567052
GO:0042723	thiamin and derivative metabolic process	0.00670482850567052
GO:0006104	succinyl-CoA metabolic process	0.00887282225080137
GO:0046459	short-chain fatty acid metabolic process	0.00887282225080137
GO:0044237	cellular metabolic process	0.012659751575851
GO:0006750	glutathione biosynthetic process	0.0158711586352915
GO:0016778	diphosphotransferase activity	0.0175881248661717
GO:0043648	dicarboxylic acid metabolic process	0.0215305804242013
GO:0016290	palmitoyl-CoA hydrolase activity	0.0251121303351356
GO:0006637	acyl-CoA metabolic process	0.0271973565350132
GO:0016291	acyl-CoA thioesterase activity	0.0271973565350132
GO:0016439	tRNA-pseudouridine synthase activity	0.0280890825215545
GO:0006100	tricarboxylic acid cycle intermediate metabolic process	0.0280890825215545
GO:0016289	CoA hydrolase activity	0.0280890825215545
GO:0005524	ATP binding	0.0280890825215545
GO:0032559	adenyl ribonucleotide binding	0.0280890825215545
GO:0048535	lymph node development	0.0280890825215545
GO:0009982	pseudouridine synthase activity	0.0280890825215545
GO:0006071	glycerol metabolic process	0.0280890825215545
GO:0006749	glutathione metabolic process	0.0280890825215545
GO:0030554	adenyl nucleotide binding	0.0280890825215545
GO:0019751	polyol metabolic process	0.0286642222772942
GO:0046632	alpha-beta T cell differentiation	0.0292573863030531
GO:0043565	sequence-specific DNA binding	0.0319626946343949
GO:0033077	T cell differentiation in the thymus	0.0329789809096057
GO:0016866	intramolecular transferase activity	0.0361091449643436
GO:0044272	sulfur compound biosynthetic process	0.0361091449643436
GO:0032553	ribonucleotide binding	0.0361091449643436
GO:0032555	purine ribonucleotide binding	0.0361091449643436
GO:0046631	alpha-beta T cell activation	0.0361091449643436
GO:0017076	purine nucleotide binding	0.039258165142745
GO:0006767	water-soluble vitamin metabolic process	0.0433610996112219
GO:0006629	lipid metabolic process	0.0464976064349754
GO:0005496	steroid binding	0.0499772616505179

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>disease_data<br>

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Cell Type

Ontology term	p-value	n

Uber Anatomy

Ontology term	p-value	n

Disease

Ontology term	p-value	n

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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