MCL coexpression mm9:3384

Phase1 CAGE Peaks

	Short description
Mm9::chr3:108248065..108248096,-	p1@Sars
Mm9::chr3:108248101..108248129,-	p2@Sars
Mm9::chr4:128867107..128867200,+	p1@Yars

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:0043038	amino acid activation	5.53017928454632e-05
GO:0043039	tRNA aminoacylation	5.53017928454632e-05
GO:0006418	tRNA aminoacylation for protein translation	5.53017928454632e-05
GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	5.53017928454632e-05
GO:0016875	ligase activity, forming carbon-oxygen bonds	5.53017928454632e-05
GO:0004812	aminoacyl-tRNA ligase activity	5.53017928454632e-05
GO:0006399	tRNA metabolic process	0.000199521774478894
GO:0006520	amino acid metabolic process	0.000803815791288871
GO:0006434	seryl-tRNA aminoacylation	0.000858282884454908
GO:0004828	serine-tRNA ligase activity	0.000858282884454908
GO:0004831	tyrosine-tRNA ligase activity	0.000858282884454908
GO:0006437	tyrosyl-tRNA aminoacylation	0.000858282884454908
GO:0006519	amino acid and derivative metabolic process	0.00085993419714682
GO:0016874	ligase activity	0.00100874984582194
GO:0009308	amine metabolic process	0.00100874984582194
GO:0006807	nitrogen compound metabolic process	0.00109559623274966
GO:0006412	translation	0.00148691136252163
GO:0019752	carboxylic acid metabolic process	0.00148691136252163
GO:0006082	organic acid metabolic process	0.00148691136252163
GO:0009059	macromolecule biosynthetic process	0.00288472209210212
GO:0000049	tRNA binding	0.00294187802669021
GO:0044249	cellular biosynthetic process	0.0045300786801657
GO:0009058	biosynthetic process	0.00793648198463862
GO:0005524	ATP binding	0.00876794125052577
GO:0032559	adenyl ribonucleotide binding	0.00876794125052577
GO:0030554	adenyl nucleotide binding	0.00929024541403085
GO:0032553	ribonucleotide binding	0.0121595522398973
GO:0032555	purine ribonucleotide binding	0.0121595522398973
GO:0017076	purine nucleotide binding	0.0126960618437547
GO:0000166	nucleotide binding	0.0157397084846313
GO:0016070	RNA metabolic process	0.0223576884150985
GO:0044267	cellular protein metabolic process	0.029193421430314
GO:0044260	cellular macromolecule metabolic process	0.029193421430314
GO:0010467	gene expression	0.029193421430314
GO:0019538	protein metabolic process	0.02967869063179
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0335849292761187

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
non-terminally differentiated cell	1.24e-12	49
ectodermal cell	1.20e-11	44
neurectodermal cell	1.20e-11	44
neural cell	1.21e-11	43
electrically responsive cell	1.20e-10	39
electrically active cell	1.20e-10	39
CNS neuron (sensu Vertebrata)	1.62e-10	23
neuroblast (sensu Vertebrata)	1.62e-10	23
neuron	9.86e-10	33
neuronal stem cell	9.86e-10	33
neuroblast	9.86e-10	33
electrically signaling cell	9.86e-10	33

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	1.89e-23	95
ectoderm	1.89e-23	95
presumptive ectoderm	1.89e-23	95
nervous system	1.52e-22	75
central nervous system	1.28e-21	73
regional part of nervous system	6.46e-19	54
ecto-epithelium	3.22e-18	73
neural tube	5.06e-18	52
neural rod	5.06e-18	52
future spinal cord	5.06e-18	52
neural keel	5.06e-18	52
neurectoderm	7.94e-18	64
neural plate	7.94e-18	64
presumptive neural plate	7.94e-18	64
gray matter	4.93e-16	34
brain	6.71e-16	47
future brain	6.71e-16	47
regional part of brain	1.47e-15	46
brain grey matter	2.56e-14	29
regional part of telencephalon	2.56e-14	29
telencephalon	2.56e-14	29
anterior neural tube	1.69e-13	40
pre-chordal neural plate	2.97e-13	49
regional part of forebrain	5.94e-13	39
forebrain	5.94e-13	39
future forebrain	5.94e-13	39
structure with developmental contribution from neural crest	2.18e-11	92
cerebral cortex	6.13e-11	21
cerebral hemisphere	6.13e-11	21
pallium	6.13e-11	21
regional part of cerebral cortex	1.40e-09	17
occipital lobe	5.64e-07	10
visual cortex	5.64e-07	10
neocortex	5.64e-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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