MCL coexpression mm9:3042

Phase1 CAGE Peaks

	Short description
Mm9::chr16:35541361..35541425,+	p1@Sema5b
Mm9::chr3:94964371..94964427,+	p1@Sema6c
Mm9::chr3:94964891..94964895,+	p@chr3:94964891..94964895 +

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:0007399	nervous system development	0.0217461573508419
GO:0048731	system development	0.032358021051397
GO:0048869	cellular developmental process	0.032358021051397
GO:0030154	cell differentiation	0.032358021051397
GO:0048856	anatomical structure development	0.032358021051397
GO:0005615	extracellular space	0.032358021051397
GO:0044421	extracellular region part	0.032358021051397
GO:0007275	multicellular organismal development	0.032358021051397
GO:0032502	developmental process	0.0498043738766139

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)	1.79e-11	23
neuroblast (sensu Vertebrata)	1.79e-11	23
neuron	1.10e-07	33
neuronal stem cell	1.10e-07	33
neuroblast	1.10e-07	33
electrically signaling cell	1.10e-07	33

Uber Anatomy

Ontology term	p-value	n
neurectoderm	5.64e-14	64
neural plate	5.64e-14	64
presumptive neural plate	5.64e-14	64
ecto-epithelium	9.29e-13	73
regional part of nervous system	2.16e-12	54
neural tube	2.60e-12	52
neural rod	2.60e-12	52
future spinal cord	2.60e-12	52
neural keel	2.60e-12	52
ectoderm-derived structure	9.01e-12	95
ectoderm	9.01e-12	95
presumptive ectoderm	9.01e-12	95
structure with developmental contribution from neural crest	1.01e-11	92
pre-chordal neural plate	1.82e-11	49
central nervous system	2.43e-11	73
multi-cellular organism	7.03e-11	333
nervous system	1.54e-10	75
brain	3.81e-10	47
future brain	3.81e-10	47
gray matter	3.97e-10	34
regional part of brain	9.88e-10	46
gonad	2.76e-09	18
gonad primordium	2.76e-09	18
anterior neural tube	4.60e-09	40
regional part of forebrain	9.16e-09	39
forebrain	9.16e-09	39
future forebrain	9.16e-09	39
external genitalia	9.21e-09	17
indifferent external genitalia	9.21e-09	17
indifferent gonad	9.21e-09	17
embryo	3.59e-08	320
testis	7.56e-08	14
brain grey matter	9.71e-08	29
regional part of telencephalon	9.71e-08	29
telencephalon	9.71e-08	29
reproductive organ	1.38e-07	24
male reproductive organ	2.30e-07	15
reproductive structure	5.50e-07	26
reproductive system	5.50e-07	26

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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