MCL coexpression mm9:2774

Phase1 CAGE Peaks

	Short description
Mm9::chr12:119539843..119539899,-	p1@Sp4
Mm9::chr12:119539902..119539931,-	p2@Sp4
Mm9::chr9:44689360..44689406,-	p1@Mll1

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:0051569	regulation of histone H3-K4 methylation	0.00602640661809018
GO:0051568	histone H3-K4 methylation	0.00602640661809018
GO:0031060	regulation of histone methylation	0.00803498870553531
GO:0031056	regulation of histone modification	0.0120518227025482
GO:0035162	embryonic hemopoiesis	0.0144613948161521
GO:0006306	DNA methylation	0.0225903576485567
GO:0006305	DNA alkylation	0.0225903576485567
GO:0016571	histone methylation	0.0225903576485567
GO:0006304	DNA modification	0.0240944004245295
GO:0051052	regulation of DNA metabolic process	0.0246237656104948
GO:0044428	nuclear part	0.0246237656104948
GO:0008213	protein amino acid alkylation	0.0246237656104948
GO:0006479	protein amino acid methylation	0.0246237656104948
GO:0016570	histone modification	0.0246237656104948
GO:0008016	regulation of heart contraction	0.0246237656104948
GO:0048568	embryonic organ development	0.0246237656104948
GO:0016569	covalent chromatin modification	0.0246237656104948
GO:0043414	biopolymer methylation	0.0246237656104948
GO:0040029	regulation of gene expression, epigenetic	0.0246237656104948
GO:0060047	heart contraction	0.0246237656104948
GO:0003015	heart process	0.0246237656104948
GO:0032259	methylation	0.0246237656104948
GO:0051128	regulation of cellular component organization and biogenesis	0.0282568237247241
GO:0003713	transcription coactivator activity	0.033112143142528
GO:0003702	RNA polymerase II transcription factor activity	0.033112143142528
GO:0006730	one-carbon compound metabolic process	0.033112143142528
GO:0006355	regulation of transcription, DNA-dependent	0.033112143142528
GO:0006351	transcription, DNA-dependent	0.033112143142528
GO:0032774	RNA biosynthetic process	0.033112143142528
GO:0008270	zinc ion binding	0.033112143142528
GO:0003677	DNA binding	0.033112143142528
GO:0009952	anterior/posterior pattern formation	0.033112143142528
GO:0008015	blood circulation	0.033112143142528
GO:0003013	circulatory system process	0.033112143142528
GO:0045449	regulation of transcription	0.033112143142528
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.033429706950182
GO:0006350	transcription	0.033429706950182
GO:0010468	regulation of gene expression	0.0347729438238879
GO:0031323	regulation of cellular metabolic process	0.0367158307621688
GO:0019222	regulation of metabolic process	0.0383625493068262
GO:0016070	RNA metabolic process	0.0383625493068262
GO:0003712	transcription cofactor activity	0.0383625493068262
GO:0046914	transition metal ion binding	0.0383625493068262
GO:0044446	intracellular organelle part	0.0383625493068262
GO:0044422	organelle part	0.0383625493068262
GO:0003002	regionalization	0.0383625493068262
GO:0016568	chromatin modification	0.0421229695873964
GO:0016563	transcription activator activity	0.044479128579898
GO:0008134	transcription factor binding	0.045763098535396
GO:0010467	gene expression	0.0464610196380316
GO:0003676	nucleic acid binding	0.0477746153611416
GO:0030097	hemopoiesis	0.0479378656622439

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
CNS neuron (sensu Vertebrata)	4.36e-09	23
neuroblast (sensu Vertebrata)	4.36e-09	23
neuron	2.08e-07	33
neuronal stem cell	2.08e-07	33
neuroblast	2.08e-07	33
electrically signaling cell	2.08e-07	33

Uber Anatomy

Ontology term	p-value	n
neurectoderm	5.30e-14	64
neural plate	5.30e-14	64
presumptive neural plate	5.30e-14	64
regional part of nervous system	7.86e-13	54
pre-chordal neural plate	3.08e-12	49
neural tube	6.54e-12	52
neural rod	6.54e-12	52
future spinal cord	6.54e-12	52
neural keel	6.54e-12	52
central nervous system	2.87e-11	73
brain	6.80e-11	47
future brain	6.80e-11	47
ecto-epithelium	8.50e-11	73
gray matter	2.25e-10	34
regional part of brain	2.57e-10	46
nervous system	3.65e-10	75
anterior neural tube	5.32e-10	40
regional part of forebrain	1.40e-09	39
forebrain	1.40e-09	39
future forebrain	1.40e-09	39
ectoderm-derived structure	3.08e-09	95
ectoderm	3.08e-09	95
presumptive ectoderm	3.08e-09	95
brain grey matter	3.21e-09	29
regional part of telencephalon	3.21e-09	29
telencephalon	3.21e-09	29
structure with developmental contribution from neural crest	6.77e-08	92

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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