MCL coexpression mm9:1277

Phase1 CAGE Peaks

	Short description
Mm9::chr11:116611222..116611252,-	p1@ENSMUST00000106377
Mm9::chr16:22622369..22622383,-	p@chr16:22622369..22622383 -
Mm9::chr4:106675318..106675331,+	p@chr4:106675318..106675331 +
Mm9::chr7:113496188..113496202,-	p@chr7:113496188..113496202 -
Mm9::chr9:59797503..59797513,-	p3@Nr2e3
Mm9::chr9:59797525..59797538,-	p2@Nr2e3

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:0045872	positive regulation of rhodopsin gene expression	0.0212008325669304
GO:0007468	regulation of rhodopsin gene expression	0.0212008325669304
GO:0060041	retina development in camera-type eye	0.0317881805600894
GO:0007205	protein kinase C activation	0.0317881805600894
GO:0004143	diacylglycerol kinase activity	0.0317881805600894
GO:0016439	tRNA-pseudouridine synthase activity	0.0317881805600894
GO:0042461	photoreceptor cell development	0.0317881805600894
GO:0009982	pseudouridine synthase activity	0.0317881805600894
GO:0046530	photoreceptor cell differentiation	0.0329628101206219
GO:0016866	intramolecular transferase activity	0.0353085843642717
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0353085843642717
GO:0032147	activation of protein kinase activity	0.0353085843642717
GO:0048015	phosphoinositide-mediated signaling	0.0398582512683634
GO:0019992	diacylglycerol binding	0.0398582512683634
GO:0005496	steroid binding	0.0398582512683634
GO:0003707	steroid hormone receptor activity	0.0398582512683634
GO:0004879	ligand-dependent nuclear receptor activity	0.0398582512683634

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><br>

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Cell Type

Ontology term	p-value	n
intestinal epithelial cell	1.36e-11	9
epithelial cell of alimentary canal	1.36e-11	9
brush border epithelial cell	2.06e-07	6
gut absorptive cell	2.06e-07	6
absorptive cell	2.06e-07	6
enterocyte	2.06e-07	6

Uber Anatomy

Ontology term	p-value	n
intestine	6.97e-32	31
gastrointestinal system	1.01e-25	47
mucosa	2.03e-15	15
intestinal mucosa	4.59e-13	13
anatomical wall	4.59e-13	13
wall of intestine	4.59e-13	13
gastrointestinal system mucosa	4.59e-13	13
epithelium of mucosa	1.36e-11	9
gastrointestinal system epithelium	1.36e-11	9
intestinal epithelium	1.36e-11	9
simple columnar epithelium	4.49e-09	11
organ component layer	3.71e-08	24

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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