MCL coexpression mm9:794

Phase1 CAGE Peaks

	Short description
Mm9::chr11:74710554..74710596,-	p1@Sgsm2
Mm9::chr11:98603160..98603171,+	p3@Thra
Mm9::chr11:98603185..98603208,+	p1@Thra
Mm9::chr16:91729647..91729680,+	p3@Itsn1
Mm9::chr1:196446044..196446066,+	p2@Plxna2
Mm9::chr3:55046452..55046477,+	p4@Dclk1
Mm9::chr3:55046483..55046501,+	p3@Dclk1
Mm9::chr4:117222931..117223014,+	p1@Eri3
Mm9::chr8:13907736..13907745,+	p3@Fbxo25

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:0046578	regulation of Ras protein signal transduction	0.0367190231283963
GO:0051056	regulation of small GTPase mediated signal transduction	0.0367190231283963
GO:0007265	Ras protein signal transduction	0.0367190231283963
GO:0004887	thyroid hormone receptor activity	0.0367190231283963
GO:0005083	small GTPase regulator activity	0.0367190231283963

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	2.56e-15	44
neurectodermal cell	2.56e-15	44
neural cell	4.13e-15	43
non-terminally differentiated cell	5.70e-15	49
CNS neuron (sensu Vertebrata)	1.45e-14	23
neuroblast (sensu Vertebrata)	1.45e-14	23
neuron	2.45e-14	33
neuronal stem cell	2.45e-14	33
neuroblast	2.45e-14	33
electrically signaling cell	2.45e-14	33
electrically responsive cell	6.03e-14	39
electrically active cell	6.03e-14	39
embryonic cell	8.01e-11	70

Uber Anatomy

Ontology term	p-value	n
central nervous system	3.23e-31	73
nervous system	1.17e-29	75
ectoderm-derived structure	8.49e-27	95
ectoderm	8.49e-27	95
presumptive ectoderm	8.49e-27	95
regional part of nervous system	3.34e-26	54
neural tube	5.82e-25	52
neural rod	5.82e-25	52
future spinal cord	5.82e-25	52
neural keel	5.82e-25	52
neurectoderm	6.45e-25	64
neural plate	6.45e-25	64
presumptive neural plate	6.45e-25	64
ecto-epithelium	5.98e-23	73
brain	1.52e-21	47
future brain	1.52e-21	47
regional part of brain	4.80e-21	46
gray matter	1.23e-20	34
structure with developmental contribution from neural crest	3.78e-20	92
pre-chordal neural plate	6.99e-19	49
anterior neural tube	8.21e-19	40
regional part of forebrain	2.53e-18	39
forebrain	2.53e-18	39
future forebrain	2.53e-18	39
brain grey matter	2.52e-17	29
regional part of telencephalon	2.52e-17	29
telencephalon	2.52e-17	29
cerebral cortex	6.97e-13	21
cerebral hemisphere	6.97e-13	21
pallium	6.97e-13	21
regional part of cerebral cortex	2.17e-10	17
tube	1.20e-07	114
anatomical conduit	3.46e-07	122
occipital lobe	3.49e-07	10
visual cortex	3.49e-07	10
neocortex	3.49e-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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