MCL coexpression mm9:848

Phase1 CAGE Peaks

	Short description
Mm9::chr5:107788562..107788605,+	p2@Brdt
Mm9::chr9:43851294..43851336,+	p2@Thy1
Mm9::chr9:43851473..43851517,+	p1@Thy1
Mm9::chr9:43854810..43854849,-	p@chr9:43854810..43854849 -
Mm9::chr9:43854871..43854901,+	p@chr9:43854871..43854901 +
Mm9::chr9:43854935..43854978,-	p@chr9:43854935..43854978 -
Mm9::chr9:43854987..43854999,+	p@chr9:43854987..43854999 +
Mm9::chr9:43855655..43855666,+	p@chr9:43855655..43855666 +
Mm9::chr9:43856002..43856018,+	p@chr9:43856002..43856018 +

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:0042670	retinal cone cell differentiation	0.00597162110338027
GO:0046549	retinal cone cell development	0.00597162110338027
GO:0060042	retina morphogenesis in camera-type eye	0.00716555271254392
GO:0031362	anchored to external side of plasma membrane	0.00716555271254392
GO:0031233	intrinsic to external side of plasma membrane	0.00716555271254392
GO:0050858	negative regulation of antigen receptor-mediated signaling pathway	0.00852995250122804
GO:0050860	negative regulation of T cell receptor signaling pathway	0.00852995250122804
GO:0042393	histone binding	0.010103051914287
GO:0060041	retina development in camera-type eye	0.010103051914287
GO:0050856	regulation of T cell receptor signaling pathway	0.010103051914287
GO:0031225	anchored to membrane	0.010103051914287
GO:0046658	anchored to plasma membrane	0.010103051914287
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.010103051914287
GO:0042462	eye photoreceptor cell development	0.0119376802103351
GO:0001754	eye photoreceptor cell differentiation	0.0119376802103351
GO:0042461	photoreceptor cell development	0.0119376802103351
GO:0048593	camera-type eye morphogenesis	0.0119376802103351
GO:0050852	T cell receptor signaling pathway	0.0119376802103351
GO:0046530	photoreceptor cell differentiation	0.0131931932796124
GO:0050851	antigen receptor-mediated signaling pathway	0.0161118930923894
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0181353277613955
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0181353277613955
GO:0002757	immune response-activating signal transduction	0.0181353277613955
GO:0006338	chromatin remodeling	0.0181353277613955
GO:0002764	immune response-regulating signal transduction	0.0181353277613955
GO:0048592	eye morphogenesis	0.0197295590217139
GO:0043010	camera-type eye development	0.0327755362301843
GO:0002253	activation of immune response	0.0327755362301843
GO:0050778	positive regulation of immune response	0.0389109199577307
GO:0002684	positive regulation of immune system process	0.0389109199577307
GO:0001654	eye development	0.0399545960452431
GO:0050776	regulation of immune response	0.0401367309985071
GO:0002682	regulation of immune system process	0.0401367309985071
GO:0051240	positive regulation of multicellular organismal process	0.0401367309985071
GO:0048503	GPI anchor binding	0.0401367309985071
GO:0001525	angiogenesis	0.0437371347021604
GO:0009897	external side of plasma membrane	0.0437371347021604
GO:0016043	cellular component organization and biogenesis	0.0460427918832516
GO:0035091	phosphoinositide binding	0.04904453936278
GO:0016568	chromatin modification	0.04904453936278
GO:0048514	blood vessel morphogenesis	0.0491152203408847
GO:0009986	cell surface	0.0491152203408847
GO:0000904	cellular morphogenesis during differentiation	0.0491152203408847
GO:0048646	anatomical structure formation	0.0491152203408847
GO:0007423	sensory organ development	0.0491152203408847

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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