MCL coexpression mm9:2539

Phase1 CAGE Peaks

	Short description
Mm9::chr10:13685585..13685645,+	p2@Hivep2
Mm9::chr10:13685899..13685916,+	p1@Hivep2
Mm9::chrX:12339216..12339239,-	p4@Med14

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:0044451	nucleoplasm part	0.0202373801242691
GO:0005654	nucleoplasm	0.0202373801242691
GO:0031981	nuclear lumen	0.0202373801242691
GO:0031974	membrane-enclosed lumen	0.0202373801242691
GO:0043233	organelle lumen	0.0202373801242691
GO:0000119	mediator complex	0.0241471748558044
GO:0044428	nuclear part	0.0255491761587703
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	0.0414820964828024
GO:0043234	protein complex	0.0414820964828024
GO:0003713	transcription coactivator activity	0.0414820964828024
GO:0006355	regulation of transcription, DNA-dependent	0.0414820964828024
GO:0006351	transcription, DNA-dependent	0.0414820964828024
GO:0032774	RNA biosynthetic process	0.0414820964828024
GO:0045449	regulation of transcription	0.0414820964828024
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0414820964828024
GO:0006350	transcription	0.0414820964828024
GO:0032991	macromolecular complex	0.0414820964828024
GO:0010468	regulation of gene expression	0.0414820964828024
GO:0031323	regulation of cellular metabolic process	0.0414820964828024
GO:0019222	regulation of metabolic process	0.0414820964828024
GO:0016070	RNA metabolic process	0.0414820964828024
GO:0003712	transcription cofactor activity	0.0414820964828024
GO:0044446	intracellular organelle part	0.0414820964828024
GO:0044422	organelle part	0.0414820964828024
GO:0016563	transcription activator activity	0.0483065873043917
GO:0008134	transcription factor binding	0.0483065873043917
GO:0010467	gene expression	0.0483065873043917
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0483065873043917

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	3.12e-07	33
neuronal stem cell	3.12e-07	33
neuroblast	3.12e-07	33
electrically signaling cell	3.12e-07	33

Uber Anatomy

Ontology term	p-value	n
gray matter	2.94e-13	34
organ part	1.86e-12	99
brain grey matter	1.12e-11	29
regional part of telencephalon	1.12e-11	29
telencephalon	1.12e-11	29
cerebral cortex	6.12e-11	21
cerebral hemisphere	6.12e-11	21
pallium	6.12e-11	21
nervous system	1.26e-10	75
regional part of nervous system	1.40e-10	54
central nervous system	1.96e-10	73
neural tube	4.30e-10	52
neural rod	4.30e-10	52
future spinal cord	4.30e-10	52
neural keel	4.30e-10	52
ectoderm-derived structure	1.57e-09	95
ectoderm	1.57e-09	95
presumptive ectoderm	1.57e-09	95
brain	4.29e-09	47
future brain	4.29e-09	47
regional part of forebrain	1.05e-08	39
forebrain	1.05e-08	39
future forebrain	1.05e-08	39
regional part of cerebral cortex	1.07e-08	17
anterior neural tube	1.22e-08	40
ecto-epithelium	1.24e-08	73
regional part of brain	1.44e-08	46
occipital lobe	4.47e-08	10
visual cortex	4.47e-08	10
neocortex	4.47e-08	10
neurectoderm	4.80e-08	64
neural plate	4.80e-08	64
presumptive neural plate	4.80e-08	64

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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