MCL coexpression mm9:483

Phase1 CAGE Peaks

	Short description
Mm9::chr10:91627958..91627984,-	p2@Rmst
Mm9::chr11:47802464..47802482,-	p7@Sgcd
Mm9::chr18:59222142..59222192,+	p1@A730017C20Rik
Mm9::chr7:13365956..13366028,-	p@chr7:13365956..13366028 -
Mm9::chr7:6683274..6683357,+	p1@Usp29
Mm9::chr7:6683398..6683427,+	p2@Usp29
Mm9::chr8:114535292..114535347,+	p1@Terf2ip
Mm9::chr9:111174336..111174418,+	p1@Epm2aip1
Mm9::chr9:111174424..111174447,+	p2@Epm2aip1
Mm9::chr9:45792860..45792891,-	p2@Pafah1b2
Mm9::chrX:132330652..132330703,+	p2@Gprasp1
Mm9::chrX:132373579..132373614,+	p1@Gprasp2
Mm9::chrX:132373618..132373625,+	p2@Gprasp2
Mm9::chrX:20281048..20281077,+	p1@Usp11
Mm9::chrX:7151370..7151438,-	p2@Ppp1r3f

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:0004221	ubiquitin thiolesterase activity	0.0191150467997155
GO:0004843	ubiquitin-specific protease activity	0.0191150467997155
GO:0019783	small conjugating protein-specific protease activity	0.0191150467997155
GO:0016790	thiolester hydrolase activity	0.0219964618309032
GO:0006511	ubiquitin-dependent protein catabolic process	0.0219964618309032
GO:0043632	modification-dependent macromolecule catabolic process	0.0219964618309032
GO:0019941	modification-dependent protein catabolic process	0.0219964618309032
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0219964618309032
GO:0044257	cellular protein catabolic process	0.0219964618309032
GO:0008234	cysteine-type peptidase activity	0.0283538819435009
GO:0016012	sarcoglycan complex	0.0283538819435009
GO:0016011	dystroglycan complex	0.0285738468227538
GO:0030163	protein catabolic process	0.0285738468227538
GO:0044265	cellular macromolecule catabolic process	0.0398502399423991
GO:0016010	dystrophin-associated glycoprotein complex	0.0398502399423991
GO:0043285	biopolymer catabolic process	0.0398502399423991

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)	3.17e-13	23
neuroblast (sensu Vertebrata)	3.17e-13	23
neuron	1.92e-12	33
neuronal stem cell	1.92e-12	33
neuroblast	1.92e-12	33
electrically signaling cell	1.92e-12	33
electrically responsive cell	2.25e-09	39
electrically active cell	2.25e-09	39
ectodermal cell	8.38e-07	44
neurectodermal cell	8.38e-07	44

Uber Anatomy

Ontology term	p-value	n
neurectoderm	9.29e-26	64
neural plate	9.29e-26	64
presumptive neural plate	9.29e-26	64
regional part of nervous system	1.19e-24	54
central nervous system	2.67e-24	73
neural tube	4.31e-23	52
neural rod	4.31e-23	52
future spinal cord	4.31e-23	52
neural keel	4.31e-23	52
nervous system	1.40e-22	75
ecto-epithelium	3.61e-22	73
ectoderm-derived structure	3.60e-21	95
ectoderm	3.60e-21	95
presumptive ectoderm	3.60e-21	95
pre-chordal neural plate	4.44e-21	49
structure with developmental contribution from neural crest	4.73e-21	92
brain	7.93e-20	47
future brain	7.93e-20	47
regional part of brain	3.26e-19	46
anterior neural tube	2.11e-18	40
regional part of forebrain	1.13e-17	39
forebrain	1.13e-17	39
future forebrain	1.13e-17	39
gray matter	2.33e-15	34
brain grey matter	2.36e-12	29
regional part of telencephalon	2.36e-12	29
telencephalon	2.36e-12	29
multi-cellular organism	2.42e-08	333
cerebral cortex	1.26e-07	21
cerebral hemisphere	1.26e-07	21
pallium	1.26e-07	21
tube	9.66e-07	114

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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