MCL coexpression mm9:3139

Phase1 CAGE Peaks

	Short description
Mm9::chr18:37844883..37844943,+	p1@Pcdhga4
Mm9::chr18:37874393..37874474,+	p1@Pcdhga7
Mm9::chr9:96632719..96632745,-	p7@Zbtb38

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:0005624	membrane fraction	0.0182492959171436
GO:0000267	cell fraction	0.0182492959171436
GO:0022610	biological adhesion	0.0182492959171436
GO:0007155	cell adhesion	0.0182492959171436
GO:0043169	cation binding	0.0210997221875286
GO:0005509	calcium ion binding	0.0210997221875286
GO:0046872	metal ion binding	0.0210997221875286
GO:0043167	ion binding	0.0210997221875286
GO:0005515	protein binding	0.0470021974850667

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
non-terminally differentiated cell	3.77e-12	49
ectodermal cell	8.65e-11	44
neurectodermal cell	8.65e-11	44
neural cell	1.24e-10	43
CNS neuron (sensu Vertebrata)	1.31e-10	23
neuroblast (sensu Vertebrata)	1.31e-10	23
electrically responsive cell	6.83e-10	39
electrically active cell	6.83e-10	39
neuron	1.90e-08	33
neuronal stem cell	1.90e-08	33
neuroblast	1.90e-08	33
electrically signaling cell	1.90e-08	33

Uber Anatomy

Ontology term	p-value	n
neurectoderm	3.87e-29	64
neural plate	3.87e-29	64
presumptive neural plate	3.87e-29	64
central nervous system	7.00e-29	73
nervous system	2.90e-28	75
structure with developmental contribution from neural crest	4.64e-28	92
neural tube	1.02e-27	52
neural rod	1.02e-27	52
future spinal cord	1.02e-27	52
neural keel	1.02e-27	52
regional part of nervous system	1.53e-27	54
ectoderm-derived structure	2.00e-27	95
ectoderm	2.00e-27	95
presumptive ectoderm	2.00e-27	95
ecto-epithelium	4.31e-26	73
brain	3.97e-25	47
future brain	3.97e-25	47
regional part of brain	2.00e-24	46
pre-chordal neural plate	1.27e-23	49
anterior neural tube	4.36e-21	40
regional part of forebrain	2.32e-20	39
forebrain	2.32e-20	39
future forebrain	2.32e-20	39
gray matter	1.27e-18	34
brain grey matter	2.62e-16	29
regional part of telencephalon	2.62e-16	29
telencephalon	2.62e-16	29
anatomical conduit	7.57e-15	122
tube	1.24e-14	114
cerebral cortex	4.71e-12	21
cerebral hemisphere	4.71e-12	21
pallium	4.71e-12	21
regional part of cerebral cortex	5.32e-10	17
multi-cellular organism	3.98e-08	333
posterior neural tube	4.26e-07	12
chordal neural plate	4.26e-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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