MCL coexpression mm9:2828

Phase1 CAGE Peaks

	Short description
Mm9::chr13:21545538..21545569,-	p2@Zfp187
Mm9::chr9:68501549..68501564,+	p6@Rora
Mm9::chr9:68501568..68501592,+	p3@Rora

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:0043030	regulation of macrophage activation	0.0119513702105763
GO:0042116	macrophage activation	0.0119513702105763
GO:0021692	cerebellar Purkinje cell layer morphogenesis	0.0119513702105763
GO:0021694	cerebellar Purkinje cell layer formation	0.0119513702105763
GO:0021702	cerebellar Purkinje cell differentiation	0.0119513702105763
GO:0021697	cerebellar cortex formation	0.0119513702105763
GO:0021533	cell differentiation in hindbrain	0.0119513702105763
GO:0021680	cerebellar Purkinje cell layer development	0.0119513702105763
GO:0021696	cerebellar cortex morphogenesis	0.0119513702105763
GO:0046068	cGMP metabolic process	0.0119513702105763
GO:0021587	cerebellum morphogenesis	0.0119513702105763
GO:0021575	hindbrain morphogenesis	0.0119513702105763
GO:0046209	nitric oxide metabolic process	0.0119513702105763
GO:0006809	nitric oxide biosynthetic process	0.0119513702105763
GO:0003700	transcription factor activity	0.0119513702105763
GO:0021695	cerebellar cortex development	0.0119513702105763
GO:0022037	metencephalon development	0.0135725356259295
GO:0021549	cerebellum development	0.0135725356259295
GO:0002274	myeloid leukocyte activation	0.0150927438914705
GO:0009187	cyclic nucleotide metabolic process	0.0196431301828096
GO:0030902	hindbrain development	0.0212329048452931
GO:0003707	steroid hormone receptor activity	0.0221524288309846
GO:0004879	ligand-dependent nuclear receptor activity	0.0221524288309846
GO:0044271	nitrogen compound biosynthetic process	0.0329664885539245
GO:0050865	regulation of cell activation	0.0329664885539245
GO:0006355	regulation of transcription, DNA-dependent	0.0329664885539245
GO:0006351	transcription, DNA-dependent	0.0329664885539245
GO:0032774	RNA biosynthetic process	0.0329664885539245
GO:0008270	zinc ion binding	0.0329664885539245
GO:0003677	DNA binding	0.0329664885539245
GO:0045449	regulation of transcription	0.0329664885539245
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0330521262380725
GO:0006350	transcription	0.0330521262380725
GO:0010468	regulation of gene expression	0.0342708745815109
GO:0031323	regulation of cellular metabolic process	0.0360768799411129
GO:0019222	regulation of metabolic process	0.0377164590634241
GO:0016070	RNA metabolic process	0.0386599017045434
GO:0046914	transition metal ion binding	0.0396731863729357
GO:0009117	nucleotide metabolic process	0.0473294077360537
GO:0007420	brain development	0.0473294077360537
GO:0048646	anatomical structure formation	0.0473294077360537
GO:0010467	gene expression	0.0473294077360537
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0473294077360537
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0473294077360537
GO:0003676	nucleic acid binding	0.0473294077360537
GO:0045321	leukocyte activation	0.0473294077360537
GO:0001775	cell activation	0.0496748534331398
GO:0007417	central nervous system development	0.0499057757583858
GO:0045893	positive regulation of transcription, DNA-dependent	0.0499057757583858
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0499057757583858

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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