MCL coexpression mm9:1874

Phase1 CAGE Peaks

	Short description
Mm9::chr10:126632769..126632795,-	p1@Dtx3
Mm9::chr19:4906598..4906632,-	p1@Bbs1
Mm9::chr2:91284786..91284883,-	p1@1110051M20Rik
Mm9::chr4:151852285..151852292,+	p3@Nphp4

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:0001895	retinal homeostasis	0.0150643656558385
GO:0035058	sensory cilium biogenesis	0.0150643656558385
GO:0042384	cilium biogenesis	0.0281132154888067
GO:0001894	tissue homeostasis	0.0313158528520386
GO:0048871	multicellular organismal homeostasis	0.0313158528520386
GO:0016358	dendrite development	0.0376144828755884
GO:0030031	cell projection biogenesis	0.0376144828755884
GO:0007219	Notch signaling pathway	0.0376144828755884
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0427804872174396

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
ectodermal cell	7.09e-13	44
neurectodermal cell	7.09e-13	44
neural cell	1.40e-12	43
non-terminally differentiated cell	2.27e-11	49
CNS neuron (sensu Vertebrata)	1.47e-10	23
neuroblast (sensu Vertebrata)	1.47e-10	23
neuron	3.28e-10	33
neuronal stem cell	3.28e-10	33
neuroblast	3.28e-10	33
electrically signaling cell	3.28e-10	33
electrically responsive cell	5.63e-09	39
electrically active cell	5.63e-09	39

Uber Anatomy

Ontology term	p-value	n
central nervous system	4.08e-33	73
nervous system	7.52e-32	75
neurectoderm	1.96e-30	64
neural plate	1.96e-30	64
presumptive neural plate	1.96e-30	64
ectoderm-derived structure	1.17e-29	95
ectoderm	1.17e-29	95
presumptive ectoderm	1.17e-29	95
regional part of nervous system	1.94e-28	54
neural tube	2.23e-27	52
neural rod	2.23e-27	52
future spinal cord	2.23e-27	52
neural keel	2.23e-27	52
ecto-epithelium	3.78e-26	73
brain	1.36e-25	47
future brain	1.36e-25	47
pre-chordal neural plate	4.21e-25	49
regional part of brain	7.39e-25	46
structure with developmental contribution from neural crest	1.19e-22	92
anterior neural tube	8.29e-22	40
regional part of forebrain	4.15e-21	39
forebrain	4.15e-21	39
future forebrain	4.15e-21	39
gray matter	1.09e-17	34
brain grey matter	7.20e-16	29
regional part of telencephalon	7.20e-16	29
telencephalon	7.20e-16	29
cerebral cortex	1.66e-11	21
cerebral hemisphere	1.66e-11	21
pallium	1.66e-11	21
regional part of cerebral cortex	5.60e-10	17
tube	9.98e-10	114
anatomical conduit	1.62e-09	122
occipital lobe	3.19e-07	10
visual cortex	3.19e-07	10
neocortex	3.19e-07	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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