MCL coexpression mm9:1956

Phase1 CAGE Peaks

	Short description
Mm9::chr11:118884346..118884418,+	p1@Cbx2
Mm9::chr12:3891753..3891801,+	p4@Dnmt3a
Mm9::chr12:3891810..3891829,+	p2@Dnmt3a
Mm9::chr8:49640232..49640254,-	p@chr8:49640232..49640254 -

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:0003682	chromatin binding	0.00187233668768843
GO:0006333	chromatin assembly or disassembly	0.00187233668768843
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.00187233668768843
GO:0016568	chromatin modification	0.00187233668768843
GO:0045892	negative regulation of transcription, DNA-dependent	0.00187233668768843
GO:0000785	chromatin	0.00187233668768843
GO:0016481	negative regulation of transcription	0.00226614584528352
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00226614584528352
GO:0006325	establishment and/or maintenance of chromatin architecture	0.00226614584528352
GO:0006323	DNA packaging	0.00226614584528352
GO:0031324	negative regulation of cellular metabolic process	0.00226614584528352
GO:0044427	chromosomal part	0.00226614584528352
GO:0009892	negative regulation of metabolic process	0.00253188015870781
GO:0005694	chromosome	0.00260370928974837
GO:0051276	chromosome organization and biogenesis	0.00260370928974837
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.00260370928974837
GO:0006346	methylation-dependent chromatin silencing	0.00260370928974837
GO:0006366	transcription from RNA polymerase II promoter	0.00276636532952671
GO:0009008	DNA-methyltransferase activity	0.00276636532952671
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	0.00276636532952671
GO:0006349	genetic imprinting	0.00368828499715308
GO:0006259	DNA metabolic process	0.00510240410109346
GO:0031519	PcG protein complex	0.00529130720520893
GO:0006342	chromatin silencing	0.00575277872598862
GO:0031507	heterochromatin formation	0.00575277872598862
GO:0045814	negative regulation of gene expression, epigenetic	0.00592630161689409
GO:0006306	DNA methylation	0.00592630161689409
GO:0006305	DNA alkylation	0.00592630161689409
GO:0006304	DNA modification	0.00675352894215406
GO:0048523	negative regulation of cellular process	0.00675352894215406
GO:0048519	negative regulation of biological process	0.00754741719645139
GO:0005720	nuclear heterochromatin	0.00794937814688782
GO:0044428	nuclear part	0.00868844037722492
GO:0016458	gene silencing	0.00878198166395754
GO:0000790	nuclear chromatin	0.00979385574920977
GO:0006996	organelle organization and biogenesis	0.0101618830315694
GO:0000792	heterochromatin	0.0104887980357588
GO:0006338	chromatin remodeling	0.0104887980357588
GO:0016569	covalent chromatin modification	0.0104887980357588
GO:0043414	biopolymer methylation	0.0115931577514032
GO:0040029	regulation of gene expression, epigenetic	0.0115931577514032
GO:0032259	methylation	0.0118428586983809
GO:0043232	intracellular non-membrane-bound organelle	0.0147372239141137
GO:0043228	non-membrane-bound organelle	0.0147372239141137
GO:0044454	nuclear chromosome part	0.0164472570636924
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0168087586770492
GO:0006730	one-carbon compound metabolic process	0.0179454118926397
GO:0000228	nuclear chromosome	0.0179454118926397
GO:0006355	regulation of transcription, DNA-dependent	0.0197442901750522
GO:0006351	transcription, DNA-dependent	0.0197442901750522
GO:0032774	RNA biosynthetic process	0.0197442901750522
GO:0003677	DNA binding	0.0198564397995261
GO:0045449	regulation of transcription	0.0200774315624076
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0204916511748874
GO:0006350	transcription	0.0206490603095587
GO:0031497	chromatin assembly	0.0208873791638374
GO:0010468	regulation of gene expression	0.0212852565225011
GO:0031323	regulation of cellular metabolic process	0.0226682848545741
GO:0019222	regulation of metabolic process	0.0239624401807811
GO:0016070	RNA metabolic process	0.0248233767474019
GO:0044446	intracellular organelle part	0.0257335423398747
GO:0044422	organelle part	0.0257335423398747
GO:0016043	cellular component organization and biogenesis	0.0257335423398747
GO:0008168	methyltransferase activity	0.0270319177716249
GO:0016741	transferase activity, transferring one-carbon groups	0.0271223901610347
GO:0010467	gene expression	0.0315666581747742
GO:0007283	spermatogenesis	0.0315666581747742
GO:0048232	male gamete generation	0.0315666581747742
GO:0003676	nucleic acid binding	0.03242253540517
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0371169613519659
GO:0007276	gamete generation	0.0387013602245768
GO:0050794	regulation of cellular process	0.0415016274214106
GO:0019953	sexual reproduction	0.0439138137767235

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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