MCL coexpression mm9:3577

Phase1 CAGE Peaks

	Short description
Mm9::chr6:83267532..83267582,-	p1@Mthfd2
Mm9::chr6:83267583..83267596,-	p2@Mthfd2
Mm9::chr7:150785954..150785983,-	p1@Cars

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:0006520	amino acid metabolic process	0.00269568024921202
GO:0006423	cysteinyl-tRNA aminoacylation	0.00269568024921202
GO:0000105	histidine biosynthetic process	0.00269568024921202
GO:0004488	methylenetetrahydrofolate dehydrogenase (NADP+) activity	0.00269568024921202
GO:0004817	cysteine-tRNA ligase activity	0.00269568024921202
GO:0004486	methylenetetrahydrofolate dehydrogenase activity	0.00269568024921202
GO:0009076	histidine family amino acid biosynthetic process	0.00269568024921202
GO:0004477	methenyltetrahydrofolate cyclohydrolase activity	0.00269568024921202
GO:0006519	amino acid and derivative metabolic process	0.00269568024921202
GO:0009308	amine metabolic process	0.00328380268959057
GO:0006807	nitrogen compound metabolic process	0.00345843917185193
GO:0019238	cyclohydrolase activity	0.00372510883533307
GO:0019752	carboxylic acid metabolic process	0.00437938331393147
GO:0006082	organic acid metabolic process	0.00437938331393147
GO:0009396	folic acid and derivative biosynthetic process	0.00521472373854911
GO:0006555	methionine metabolic process	0.00525840086881686
GO:0009086	methionine biosynthetic process	0.00525840086881686
GO:0009075	histidine family amino acid metabolic process	0.0055864385932362
GO:0006547	histidine metabolic process	0.0055864385932362
GO:0016646	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	0.0055864385932362
GO:0006760	folic acid and derivative metabolic process	0.0055864385932362
GO:0000097	sulfur amino acid biosynthetic process	0.0055864385932362
GO:0000049	tRNA binding	0.0055864385932362
GO:0009067	aspartate family amino acid biosynthetic process	0.0055864385932362
GO:0009066	aspartate family amino acid metabolic process	0.00625646831969079
GO:0000096	sulfur amino acid metabolic process	0.00687486309335938
GO:0044249	cellular biosynthetic process	0.00797887704781829
GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	0.00797887704781829
GO:0016814	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	0.00885857639858035
GO:0044272	sulfur compound biosynthetic process	0.0107954166363953
GO:0008652	amino acid biosynthetic process	0.0123796454361451
GO:0009058	biosynthetic process	0.0123796454361451
GO:0043038	amino acid activation	0.0143925238184049
GO:0043039	tRNA aminoacylation	0.0143925238184049
GO:0006418	tRNA aminoacylation for protein translation	0.0143925238184049
GO:0016875	ligase activity, forming carbon-oxygen bonds	0.0143925238184049
GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	0.0143925238184049
GO:0004812	aminoacyl-tRNA ligase activity	0.0143925238184049
GO:0006752	group transfer coenzyme metabolic process	0.0153446041292717
GO:0005625	soluble fraction	0.0153446041292717
GO:0009309	amine biosynthetic process	0.0159402589561594
GO:0006790	sulfur metabolic process	0.0159402589561594
GO:0006164	purine nucleotide biosynthetic process	0.0167345164194997
GO:0046483	heterocycle metabolic process	0.0167345164194997
GO:0006163	purine nucleotide metabolic process	0.0182718976133919
GO:0044271	nitrogen compound biosynthetic process	0.0182718976133919
GO:0006730	one-carbon compound metabolic process	0.0182718976133919
GO:0009108	coenzyme biosynthetic process	0.0192821786766828
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0204777483448519
GO:0051188	cofactor biosynthetic process	0.0214025459163666
GO:0006399	tRNA metabolic process	0.0218547738660344
GO:0006725	aromatic compound metabolic process	0.0242123242615664
GO:0009165	nucleotide biosynthetic process	0.0256411751555361
GO:0006732	coenzyme metabolic process	0.0327653977682705
GO:0009117	nucleotide metabolic process	0.0365986452977421
GO:0051186	cofactor metabolic process	0.0371305140389463
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0378373351305979
GO:0032787	monocarboxylic acid metabolic process	0.0408054310535513
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0444730834121558

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><br><br>

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Cell Type

Ontology term	p-value	n
stem cell	4.98e-09	97
somatic stem cell	1.98e-07	91
multi fate stem cell	1.98e-07	91

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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