MCL coexpression mm9:966

Phase1 CAGE Peaks

	Short description
Mm9::chr15:78744346..78744357,+	p2@Pdxp
Mm9::chr19:16207236..16207263,+	p3@Gnaq
Mm9::chr19:5093003..5093016,-	p@chr19:5093003..5093016 -
Mm9::chr1:91476758..91476777,+	p@chr1:91476758..91476777 +
Mm9::chr2:153355941..153355988,-	p3@8430427H17Rik
Mm9::chr3:89263219..89263243,+	p4@Pmvk
Mm9::chr5:24414378..24414401,-	p9@Prkag2
Mm9::chr7:54388068..54388082,-	p9@Ptpn5

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:0006695	cholesterol biosynthetic process	0.00195623805134542
GO:0016126	sterol biosynthetic process	0.00195623805134542
GO:0008203	cholesterol metabolic process	0.00476738807664171
GO:0006694	steroid biosynthetic process	0.00476738807664171
GO:0016125	sterol metabolic process	0.00476738807664171
GO:0004631	phosphomevalonate kinase activity	0.00735038989024635
GO:0050932	regulation of pigment cell differentiation	0.0102920334871923
GO:0045634	regulation of melanocyte differentiation	0.0102920334871923
GO:0008202	steroid metabolic process	0.0102920334871923
GO:0016322	neuron remodeling	0.0160319429526234
GO:0060158	dopamine receptor, phospholipase C activating pathway	0.0160319429526234
GO:0021884	forebrain neuron development	0.0176312726477465
GO:0016791	phosphoric monoester hydrolase activity	0.0176312726477465
GO:0008610	lipid biosynthetic process	0.0176312726477465
GO:0004679	AMP-activated protein kinase activity	0.0176312726477465
GO:0006066	alcohol metabolic process	0.018147850684892
GO:0021879	forebrain neuron differentiation	0.018147850684892
GO:0021872	generation of neurons in the forebrain	0.0195860098829364
GO:0042578	phosphoric ester hydrolase activity	0.0198286620026463
GO:0042551	neuron maturation	0.0198286620026463
GO:0007215	glutamate signaling pathway	0.0209804118909944
GO:0042733	embryonic digit morphogenesis	0.0260262263429269
GO:0006471	protein amino acid ADP-ribosylation	0.0299370552228139
GO:0030318	melanocyte differentiation	0.0299370552228139
GO:0050931	pigment cell differentiation	0.0299370552228139
GO:0007212	dopamine receptor signaling pathway	0.0304755625900123
GO:0021954	central nervous system neuron development	0.0342267238762276
GO:0021953	central nervous system neuron differentiation	0.0377068485994009
GO:0044255	cellular lipid metabolic process	0.0402783680354601
GO:0016776	phosphotransferase activity, phosphate group as acceptor	0.0410405751465139
GO:0048066	pigmentation during development	0.0411306312227698
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0412147581446118
GO:0009791	post-embryonic development	0.0412934949740724
GO:0005834	heterotrimeric G-protein complex	0.042655371467583
GO:0006629	lipid metabolic process	0.042717818550928
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.042717818550928
GO:0001508	regulation of action potential	0.0429220077924235
GO:0016788	hydrolase activity, acting on ester bonds	0.0429220077924235
GO:0016787	hydrolase activity	0.0478159390112852
GO:0048015	phosphoinositide-mediated signaling	0.0482845165637295

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
neuron	3.88e-16	33
neuronal stem cell	3.88e-16	33
neuroblast	3.88e-16	33
electrically signaling cell	3.88e-16	33
CNS neuron (sensu Vertebrata)	4.17e-15	23
neuroblast (sensu Vertebrata)	4.17e-15	23
ectodermal cell	3.47e-13	44
neurectodermal cell	3.47e-13	44
neural cell	4.00e-13	43
electrically responsive cell	2.09e-11	39
electrically active cell	2.09e-11	39
non-terminally differentiated cell	1.17e-09	49

Uber Anatomy

Ontology term	p-value	n
central nervous system	4.57e-28	73
nervous system	1.76e-27	75
neurectoderm	8.34e-25	64
neural plate	8.34e-25	64
presumptive neural plate	8.34e-25	64
ectoderm-derived structure	2.15e-24	95
ectoderm	2.15e-24	95
presumptive ectoderm	2.15e-24	95
regional part of nervous system	8.38e-24	54
ecto-epithelium	1.56e-22	73
neural tube	1.88e-22	52
neural rod	1.88e-22	52
future spinal cord	1.88e-22	52
neural keel	1.88e-22	52
pre-chordal neural plate	8.86e-20	49
gray matter	2.76e-19	34
brain	3.98e-19	47
future brain	3.98e-19	47
structure with developmental contribution from neural crest	5.01e-19	92
regional part of brain	1.28e-18	46
anterior neural tube	2.12e-18	40
regional part of forebrain	7.16e-18	39
forebrain	7.16e-18	39
future forebrain	7.16e-18	39
brain grey matter	6.20e-16	29
regional part of telencephalon	6.20e-16	29
telencephalon	6.20e-16	29
cerebral cortex	4.74e-11	21
cerebral hemisphere	4.74e-11	21
pallium	4.74e-11	21
regional part of cerebral cortex	7.54e-09	17

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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