MCL coexpression mm9:353

Phase1 CAGE Peaks

	Short description
Mm9::chr11:118431001..118431046,-	p4@Rbfox3
Mm9::chr11:118431276..118431314,-	p3@Rbfox3
Mm9::chr11:118431626..118431637,-	p16@Rbfox3
Mm9::chr13:33175964..33175973,+	p2@Serpinb1b
Mm9::chr13:33175982..33176015,+	p1@Serpinb1b
Mm9::chr14:33277893..33277902,-	p6@Slc18a3
Mm9::chr14:33277950..33277963,-	p1@Slc18a3
Mm9::chr14:68742893..68742913,-	p1@Nefm
Mm9::chr17:54438043..54438057,-	p1@Slc5a7
Mm9::chr2:70053872..70053879,+	p@chr2:70053872..70053879 +
Mm9::chr4:137573229..137573260,+	p@chr4:137573229..137573260 +
Mm9::chr4:137573261..137573269,+	p@chr4:137573261..137573269 +
Mm9::chr4:150371190..150371197,+	p1@Uts2
Mm9::chr7:57165440..57165441,+	p13@Slc6a5
Mm9::chr7:57165453..57165473,+	p3@Slc6a5
Mm9::chr7:57165482..57165497,+	p2@Slc6a5
Mm9::chr7:57165576..57165593,+	p5@Slc6a5
Mm9::chr7:57165602..57165612,+	p6@Slc6a5
Mm9::chr7:57165629..57165651,+	p4@Slc6a5
Mm9::chr7:57167425..57167443,+	p@chr7:57167425..57167443 +
Mm9::chr7:57215165..57215169,+	p@chr7:57215165..57215169 +
Mm9::chr7:57215305..57215314,+	p@chr7:57215305..57215314 +

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:0005275	amine transmembrane transporter activity	1.94117445984349e-05
GO:0008504	monoamine transmembrane transporter activity	4.45609887683677e-05
GO:0015370	solute:sodium symporter activity	0.00290317603935904
GO:0022804	active transmembrane transporter activity	0.00290317603935904
GO:0006836	neurotransmitter transport	0.00290317603935904
GO:0015294	solute:cation symporter activity	0.00290317603935904
GO:0015837	amine transport	0.00290317603935904
GO:0008292	acetylcholine biosynthetic process	0.00602640661809018
GO:0005307	choline:sodium symporter activity	0.00602640661809018
GO:0008291	acetylcholine metabolic process	0.00903837176009507
GO:0015871	choline transport	0.00903837176009507
GO:0015220	choline transmembrane transporter activity	0.00903837176009507
GO:0015293	symporter activity	0.00984208619353216
GO:0031133	regulation of axon diameter	0.0101667754957099
GO:0045110	intermediate filament bundle assembly	0.0101667754957099
GO:0015844	monoamine transport	0.0101667754957099
GO:0042439	ethanolamine and derivative metabolic process	0.0123921007879047
GO:0015291	secondary active transmembrane transporter activity	0.0123921007879047
GO:0022857	transmembrane transporter activity	0.014520768102974
GO:0043195	terminal button	0.0154858644013815
GO:0005883	neurofilament	0.0154858644013815
GO:0006810	transport	0.0187540123604468
GO:0060053	neurofilament cytoskeleton	0.0187540123604468
GO:0060052	neurofilament cytoskeleton organization and biogenesis	0.0187540123604468
GO:0045109	intermediate filament organization	0.0187540123604468
GO:0033267	axon part	0.0187540123604468
GO:0051234	establishment of localization	0.0192789108118965
GO:0008088	axon cargo transport	0.019346727717088
GO:0042176	regulation of protein catabolic process	0.020112330883035
GO:0048265	response to pain	0.020112330883035
GO:0031594	neuromuscular junction	0.020112330883035
GO:0007274	neuromuscular synaptic transmission	0.020112330883035
GO:0009894	regulation of catabolic process	0.020112330883035
GO:0042136	neurotransmitter biosynthetic process	0.020112330883035
GO:0007271	synaptic transmission, cholinergic	0.020112330883035
GO:0051179	localization	0.0228123038652274
GO:0045104	intermediate filament cytoskeleton organization and biogenesis	0.0248654523517968
GO:0005328	neurotransmitter:sodium symporter activity	0.0256317698159375
GO:0045103	intermediate filament-based process	0.0270483470018585
GO:0005326	neurotransmitter transporter activity	0.0270483470018585
GO:0042401	biogenic amine biosynthetic process	0.0316490147677722
GO:0033555	multicellular organismal response to stress	0.0321783707287936
GO:0008324	cation transmembrane transporter activity	0.0335335216595175
GO:0042398	amino acid derivative biosynthetic process	0.0343874727040846
GO:0050770	regulation of axonogenesis	0.0360151058030516
GO:0004601	peroxidase activity	0.0379152230653866
GO:0016684	oxidoreductase activity, acting on peroxide as acceptor	0.0379152230653866
GO:0042133	neurotransmitter metabolic process	0.0416025674897824
GO:0050767	regulation of neurogenesis	0.0495108445735055

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 of the ventral spinal cord	1.51e-08	3
CNS neuron (sensu Vertebrata)	3.15e-07	23
neuroblast (sensu Vertebrata)	3.15e-07	23

Uber Anatomy

Ontology term	p-value	n
posterior neural tube	7.37e-20	12
chordal neural plate	7.37e-20	12
spinal cord	1.15e-15	6
dorsal region element	1.15e-15	6
dorsum	1.15e-15	6
regional part of spinal cord	3.10e-13	5
gray matter of spinal cord	3.10e-13	5
regional part of nervous system	2.49e-09	54
neural tube	1.06e-08	52
neural rod	1.06e-08	52
future spinal cord	1.06e-08	52
neural keel	1.06e-08	52
ventral horn of spinal cord	1.51e-08	3
neurectoderm	2.88e-07	64
neural plate	2.88e-07	64
presumptive neural plate	2.88e-07	64
central nervous system	7.37e-07	73
segmental subdivision of hindbrain	9.41e-07	6
segmental subdivision of nervous system	9.41e-07	6
hindbrain	9.41e-07	6
presumptive hindbrain	9.41e-07	6

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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