MCL coexpression mm9:2959

Phase1 CAGE Peaks

	Short description
Mm9::chr15:103333594..103333648,+	p2@Pde1b
Mm9::chr7:108043087..108043098,-	p8@Arhgef17
Mm9::chr8:121970938..121971035,+	p1@Necab2

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:0017000	antibiotic biosynthetic process	0.0153365824918586
GO:0016999	antibiotic metabolic process	0.0153365824918586
GO:0017144	drug metabolic process	0.0153365824918586
GO:0007632	visual behavior	0.0341393564777385
GO:0008542	visual learning	0.0341393564777385
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0341393564777385
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0341393564777385
GO:0007612	learning	0.047803038389033
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.047803038389033
GO:0035023	regulation of Rho protein signal transduction	0.047803038389033
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.047803038389033
GO:0008081	phosphoric diester hydrolase activity	0.047803038389033
GO:0007611	learning and/or memory	0.047803038389033
GO:0009416	response to light stimulus	0.047803038389033
GO:0007266	Rho protein signal transduction	0.0488756573929596

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)	2.44e-13	23
neuroblast (sensu Vertebrata)	2.44e-13	23
ectodermal cell	1.10e-10	44
neurectodermal cell	1.10e-10	44
neural cell	1.20e-10	43
neuron	1.55e-10	33
neuronal stem cell	1.55e-10	33
neuroblast	1.55e-10	33
electrically signaling cell	1.55e-10	33
non-terminally differentiated cell	5.79e-07	49

Uber Anatomy

Ontology term	p-value	n
neurectoderm	3.23e-28	64
neural plate	3.23e-28	64
presumptive neural plate	3.23e-28	64
central nervous system	6.19e-27	73
nervous system	1.21e-26	75
regional part of nervous system	9.45e-26	54
ectoderm-derived structure	1.54e-24	95
ectoderm	1.54e-24	95
presumptive ectoderm	1.54e-24	95
neural tube	3.56e-24	52
neural rod	3.56e-24	52
future spinal cord	3.56e-24	52
neural keel	3.56e-24	52
pre-chordal neural plate	3.60e-23	49
ecto-epithelium	3.63e-23	73
brain	1.65e-20	47
future brain	1.65e-20	47
regional part of brain	8.07e-20	46
anterior neural tube	2.44e-18	40
regional part of forebrain	1.03e-17	39
forebrain	1.03e-17	39
future forebrain	1.03e-17	39
gray matter	2.82e-17	34
structure with developmental contribution from neural crest	1.40e-15	92
brain grey matter	9.70e-14	29
regional part of telencephalon	9.70e-14	29
telencephalon	9.70e-14	29
cerebral cortex	9.05e-09	21
cerebral hemisphere	9.05e-09	21
pallium	9.05e-09	21
regional part of cerebral cortex	4.86e-08	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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