MCL coexpression mm9:2343

Phase1 CAGE Peaks

	Short description
Mm9::chr2:26062055..26062100,-	p1@Lhx3
Mm9::chr3:128917187..128917223,+	p2@Pitx2
Mm9::chr4:114353374..114353387,+	p1@ENSMUST00000146346
Mm9::chr4:132212598..132212620,+	p2@Eya3

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:0002074	extraocular skeletal muscle development	0.0106829726957006
GO:0021526	medial motor column neuron differentiation	0.0106829726957006
GO:0021523	somatic motor neuron differentiation	0.0106829726957006
GO:0016477	cell migration	0.0106829726957006
GO:0006928	cell motility	0.0106829726957006
GO:0051674	localization of cell	0.0106829726957006
GO:0006355	regulation of transcription, DNA-dependent	0.0106829726957006
GO:0021517	ventral spinal cord development	0.0106829726957006
GO:0021522	spinal cord motor neuron differentiation	0.0106829726957006
GO:0006351	transcription, DNA-dependent	0.0106829726957006
GO:0032774	RNA biosynthetic process	0.0106829726957006
GO:0045449	regulation of transcription	0.0106829726957006
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0106829726957006
GO:0021515	cell differentiation in spinal cord	0.0106829726957006
GO:0006350	transcription	0.0106829726957006
GO:0010468	regulation of gene expression	0.0106829726957006
GO:0008045	motor axon guidance	0.0106829726957006
GO:0031323	regulation of cellular metabolic process	0.0106829726957006
GO:0005667	transcription factor complex	0.0106829726957006
GO:0007275	multicellular organismal development	0.0106829726957006
GO:0043565	sequence-specific DNA binding	0.0106829726957006
GO:0019222	regulation of metabolic process	0.0106829726957006
GO:0016070	RNA metabolic process	0.0110493901619487
GO:0021510	spinal cord development	0.0126334477114474
GO:0044451	nucleoplasm part	0.0135941983933731
GO:0005654	nucleoplasm	0.014343789265851
GO:0010467	gene expression	0.0161329466883877
GO:0001569	patterning of blood vessels	0.0175015391550872
GO:0032502	developmental process	0.0175015391550872
GO:0031981	nuclear lumen	0.0175015391550872
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.018891367133842
GO:0031974	membrane-enclosed lumen	0.0201809521190785
GO:0043233	organelle lumen	0.0201809521190785
GO:0050794	regulation of cellular process	0.0209059308120826
GO:0007368	determination of left/right symmetry	0.0209059308120826
GO:0003700	transcription factor activity	0.0209059308120826
GO:0009799	determination of symmetry	0.0209059308120826
GO:0008138	protein tyrosine/serine/threonine phosphatase activity	0.0209059308120826
GO:0009855	determination of bilateral symmetry	0.0209059308120826
GO:0009880	embryonic pattern specification	0.0232887950107526
GO:0050789	regulation of biological process	0.0243381377615282
GO:0044428	nuclear part	0.0277722567323495
GO:0030334	regulation of cell migration	0.0281446682715988
GO:0065007	biological regulation	0.0293068929892983
GO:0048754	branching morphogenesis of a tube	0.0293068929892983
GO:0051270	regulation of cell motility	0.0293068929892983
GO:0005634	nucleus	0.0293068929892983
GO:0032501	multicellular organismal process	0.0293068929892983
GO:0001763	morphogenesis of a branching structure	0.0293068929892983
GO:0040012	regulation of locomotion	0.0293068929892983
GO:0009653	anatomical structure morphogenesis	0.0295624142412393
GO:0043283	biopolymer metabolic process	0.0299229790417025
GO:0043010	camera-type eye development	0.0328926402552631
GO:0007411	axon guidance	0.0339978428144898
GO:0004725	protein tyrosine phosphatase activity	0.0363234407530172
GO:0007519	skeletal muscle development	0.0393887586386873
GO:0001654	eye development	0.0423429060598864
GO:0006470	protein amino acid dephosphorylation	0.0424084470269759
GO:0016311	dephosphorylation	0.0463684940195847
GO:0016055	Wnt receptor signaling pathway	0.0463684940195847
GO:0014706	striated muscle development	0.0463684940195847
GO:0043234	protein complex	0.0471863066083069
GO:0001525	angiogenesis	0.0496450739327506

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
pituitary gland	4.07e-11	8
gland of diencephalon	4.07e-11	8
neuroendocrine gland	4.07e-11	8
eye	3.77e-10	9
camera-type eye	3.77e-10	9
simple eye	3.77e-10	9
immature eye	3.77e-10	9
ocular region	3.77e-10	9
visual system	3.77e-10	9
face	3.77e-10	9
optic cup	3.77e-10	9
optic vesicle	3.77e-10	9
eye primordium	3.77e-10	9
diencephalon	7.29e-10	10
future diencephalon	7.29e-10	10
subdivision of head	7.79e-08	11
sense organ	5.64e-07	12
sensory system	5.64e-07	12
entire sense organ system	5.64e-07	12

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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