MCL coexpression mm9:731

Phase1 CAGE Peaks

	Short description
Mm9::chr14:13178241..13178254,-	p4@Fezf2
Mm9::chr15:43701539..43701604,-	p1@Tmem74
Mm9::chr18:69680960..69681007,+	p10@Tcf4
Mm9::chr18:69681009..69681014,+	p35@Tcf4
Mm9::chr18:69681020..69681032,+	p23@Tcf4
Mm9::chr2:29108946..29109011,-	p1@ENSMUST00000028141 p1@ENSMUST00000154682
Mm9::chr2:84727165..84727201,-	p1@Rtn4rl2
Mm9::chr6:141473179..141473193,+	p6@Slco1c1
Mm9::chr8:125276239..125276278,-	p1@uc009ntp.1
Mm9::chr8:87296263..87296314,-	p@chr8:87296263..87296314 -

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:0007409	axonogenesis	0.0165391008126874
GO:0048667	neuron morphogenesis during differentiation	0.0165391008126874
GO:0048812	neurite morphogenesis	0.0165391008126874
GO:0000904	cellular morphogenesis during differentiation	0.0165391008126874
GO:0031175	neurite development	0.0165391008126874
GO:0031103	axon regeneration	0.0165391008126874
GO:0031102	neurite regeneration	0.0165391008126874
GO:0048666	neuron development	0.0165391008126874
GO:0048678	response to axon injury	0.0165391008126874
GO:0007413	axonal fasciculation	0.0165391008126874
GO:0032990	cell part morphogenesis	0.0165391008126874
GO:0030030	cell projection organization and biogenesis	0.0165391008126874
GO:0048858	cell projection morphogenesis	0.0165391008126874
GO:0030182	neuron differentiation	0.0165391008126874
GO:0048699	generation of neurons	0.0180350152064162
GO:0031099	regeneration	0.0180350152064162
GO:0042246	tissue regeneration	0.0180350152064162
GO:0008038	neuron recognition	0.0180350152064162
GO:0022008	neurogenesis	0.0180350152064162
GO:0000902	cell morphogenesis	0.0298404205400454
GO:0032989	cellular structure morphogenesis	0.0298404205400454
GO:0016358	dendrite development	0.0483468890330197
GO:0007399	nervous system development	0.0483468890330197

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)	1.30e-13	23
neuroblast (sensu Vertebrata)	1.30e-13	23
neuron	2.44e-07	33
neuronal stem cell	2.44e-07	33
neuroblast	2.44e-07	33
electrically signaling cell	2.44e-07	33
neuron of cerebral cortex	4.65e-07	6

Uber Anatomy

Ontology term	p-value	n
gray matter	4.34e-26	34
brain grey matter	1.31e-23	29
regional part of telencephalon	1.31e-23	29
telencephalon	1.31e-23	29
neural tube	2.54e-23	52
neural rod	2.54e-23	52
future spinal cord	2.54e-23	52
neural keel	2.54e-23	52
regional part of nervous system	2.56e-23	54
neurectoderm	1.05e-21	64
neural plate	1.05e-21	64
presumptive neural plate	1.05e-21	64
brain	5.87e-21	47
future brain	5.87e-21	47
regional part of brain	4.50e-20	46
pre-chordal neural plate	4.52e-20	49
anterior neural tube	4.73e-20	40
central nervous system	6.98e-20	73
regional part of forebrain	1.16e-19	39
forebrain	1.16e-19	39
future forebrain	1.16e-19	39
nervous system	7.12e-19	75
cerebral cortex	8.15e-19	21
cerebral hemisphere	8.15e-19	21
pallium	8.15e-19	21
ecto-epithelium	1.03e-17	73
ectoderm-derived structure	4.44e-16	95
ectoderm	4.44e-16	95
presumptive ectoderm	4.44e-16	95
regional part of cerebral cortex	7.78e-15	17
structure with developmental contribution from neural crest	8.38e-12	92
occipital lobe	3.24e-11	10
visual cortex	3.24e-11	10
neocortex	3.24e-11	10

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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