MCL coexpression mm9:959

Phase1 CAGE Peaks

	Short description
Mm9::chr15:27955589..27955634,-	p1@Trio
Mm9::chr15:27955649..27955679,-	p2@Trio
Mm9::chr15:76701830..76701883,-	p1@Zfp251
Mm9::chr1:178744201..178744264,-	p1@Cep170
Mm9::chr2:124949317..124949353,-	p1@Myef2
Mm9::chr2:124949354..124949384,-	p2@Myef2
Mm9::chr6:92041399..92041417,+	p2@Nr2c2
Mm9::chrX:13423601..13423619,-	p3@Cask

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:0048136	male germ-line cyst formation	0.0140250917657371
GO:0048134	germ-line cyst formation	0.0140250917657371
GO:0048137	spermatocyte division	0.0140250917657371

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
neuron	7.36e-16	33
neuronal stem cell	7.36e-16	33
neuroblast	7.36e-16	33
electrically signaling cell	7.36e-16	33
electrically responsive cell	3.70e-14	39
electrically active cell	3.70e-14	39
CNS neuron (sensu Vertebrata)	2.48e-11	23
neuroblast (sensu Vertebrata)	2.48e-11	23
ectodermal cell	3.21e-10	44
neurectodermal cell	3.21e-10	44
neural cell	4.32e-10	43
non-terminally differentiated cell	2.23e-09	49

Uber Anatomy

Ontology term	p-value	n
nervous system	4.76e-23	75
central nervous system	2.49e-22	73
ectoderm-derived structure	1.47e-21	95
ectoderm	1.47e-21	95
presumptive ectoderm	1.47e-21	95
neurectoderm	1.05e-20	64
neural plate	1.05e-20	64
presumptive neural plate	1.05e-20	64
ecto-epithelium	2.88e-18	73
structure with developmental contribution from neural crest	2.98e-18	92
regional part of nervous system	6.18e-18	54
neural tube	2.44e-17	52
neural rod	2.44e-17	52
future spinal cord	2.44e-17	52
neural keel	2.44e-17	52
pre-chordal neural plate	5.26e-17	49
gray matter	1.22e-15	34
brain	1.57e-15	47
future brain	1.57e-15	47
anterior neural tube	4.17e-15	40
regional part of brain	4.86e-15	46
regional part of forebrain	1.24e-14	39
forebrain	1.24e-14	39
future forebrain	1.24e-14	39
brain grey matter	1.20e-13	29
regional part of telencephalon	1.20e-13	29
telencephalon	1.20e-13	29
multi-cellular organism	4.75e-11	333
cerebral cortex	1.62e-10	21
cerebral hemisphere	1.62e-10	21
pallium	1.62e-10	21
embryo	1.52e-09	320
regional part of cerebral cortex	4.34e-08	17
tube	5.03e-07	114
occipital lobe	6.14e-07	10
visual cortex	6.14e-07	10
neocortex	6.14e-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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