MCL coexpression mm9:819

Phase1 CAGE Peaks

	Short description
Mm9::chr14:122873784..122873795,+	p@chr14:122873784..122873795 +
Mm9::chr14:122874593..122874610,+	p2@Zic2
Mm9::chr9:91255836..91255853,-	p@chr9:91255836..91255853 -
Mm9::chr9:91256536..91256556,-	p@chr9:91256536..91256556 -
Mm9::chr9:91256573..91256584,-	p@chr9:91256573..91256584 -
Mm9::chr9:91256933..91256954,+	p4@Zic4
Mm9::chr9:91257451..91257460,-	p@chr9:91257451..91257460 -
Mm9::chr9:91260594..91260612,-	p1@Zic1
Mm9::chr9:91260616..91260653,-	p2@Zic1

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:0007417	central nervous system development	0.0206579680104003
GO:0008270	zinc ion binding	0.0206579680104003
GO:0003677	DNA binding	0.0206579680104003
GO:0046914	transition metal ion binding	0.0236530812754747
GO:0008589	regulation of smoothened signaling pathway	0.0236530812754747
GO:0003676	nucleic acid binding	0.0287686637232217
GO:0007399	nervous system development	0.0287686637232217
GO:0007224	smoothened signaling pathway	0.0310192156016182
GO:0048066	pigmentation during development	0.0310192156016182
GO:0043169	cation binding	0.0310192156016182
GO:0046872	metal ion binding	0.0311320280117044
GO:0043167	ion binding	0.0311320280117044
GO:0001843	neural tube closure	0.0311320280117044
GO:0014020	primary neural tube formation	0.0311320280117044
GO:0001841	neural tube formation	0.0311320280117044
GO:0001839	neural plate morphogenesis	0.0311320280117044
GO:0001838	embryonic epithelial tube formation	0.0311320280117044
GO:0001840	neural plate development	0.0311320280117044
GO:0005634	nucleus	0.0315723399114208
GO:0021915	neural tube development	0.0319372748698152
GO:0016331	morphogenesis of embryonic epithelium	0.0341450274207378

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
CNS neuron (sensu Vertebrata)	8.26e-15	23
neuroblast (sensu Vertebrata)	8.26e-15	23
neural cell	8.55e-12	43
ectodermal cell	2.56e-11	44
neurectodermal cell	2.56e-11	44
non-terminally differentiated cell	2.92e-09	49
neuron	2.82e-08	33
neuronal stem cell	2.82e-08	33
neuroblast	2.82e-08	33
electrically signaling cell	2.82e-08	33

Uber Anatomy

Ontology term	p-value	n
neurectoderm	3.23e-23	64
neural plate	3.23e-23	64
presumptive neural plate	3.23e-23	64
central nervous system	1.04e-22	73
regional part of nervous system	2.24e-22	54
ectoderm-derived structure	3.27e-22	95
ectoderm	3.27e-22	95
presumptive ectoderm	3.27e-22	95
nervous system	1.19e-21	75
neural tube	2.99e-20	52
neural rod	2.99e-20	52
future spinal cord	2.99e-20	52
neural keel	2.99e-20	52
ecto-epithelium	2.93e-19	73
brain	9.52e-16	47
future brain	9.52e-16	47
pre-chordal neural plate	4.78e-15	49
regional part of brain	5.04e-15	46
posterior neural tube	5.81e-12	12
chordal neural plate	5.81e-12	12
structure with developmental contribution from neural crest	1.57e-11	92
anterior neural tube	8.72e-11	40
regional part of forebrain	2.59e-10	39
forebrain	2.59e-10	39
future forebrain	2.59e-10	39
gray matter	3.68e-10	34
spinal cord	3.28e-07	6
dorsal region element	3.28e-07	6
dorsum	3.28e-07	6
regional part of spinal cord	9.76e-07	5
gray matter of spinal cord	9.76e-07	5
basal ganglion	9.96e-07	8
nuclear complex of neuraxis	9.96e-07	8
aggregate regional part of brain	9.96e-07	8
collection of basal ganglia	9.96e-07	8
cerebral subcortex	9.96e-07	8

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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