MCL coexpression mm9:912

Phase1 CAGE Peaks

	Short description
Mm9::chr11:68829575..68829637,+	p1@1500010J02Rik
Mm9::chr2:156666727..156666753,+	p2@Tgif2
Mm9::chr2:84877369..84877459,+	p1@Ssrp1
Mm9::chr3:90280043..90280142,+	p1@Ilf2
Mm9::chr5:31797109..31797151,+	p1@Gpn1
Mm9::chr7:13609469..13609537,+	p3@Trim28
Mm9::chr7:52241683..52241722,-	p1@Prmt1
Mm9::chr8:81032775..81032808,-	p1@Rbmxl1

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:0019919	peptidyl-arginine methylation, to asymmetrical-dimethyl arginine	0.00848079767709418
GO:0016275	[cytochrome c]-arginine N-methyltransferase activity	0.00848079767709418
GO:0035242	protein-arginine omega-N asymmetric methyltransferase activity	0.00848079767709418
GO:0035247	peptidyl-arginine omega-N-methylation	0.00848079767709418
GO:0035241	protein-arginine omega-N monomethyltransferase activity	0.00848079767709418
GO:0018216	peptidyl-arginine methylation	0.0115615562661957
GO:0035246	peptidyl-arginine N-methylation	0.0115615562661957
GO:0016273	arginine N-methyltransferase activity	0.0115615562661957
GO:0018195	peptidyl-arginine modification	0.0115615562661957
GO:0008469	histone-arginine N-methyltransferase activity	0.0115615562661957
GO:0016274	protein-arginine N-methyltransferase activity	0.0115615562661957
GO:0043193	positive regulation of gene-specific transcription	0.0117724336002034
GO:0003677	DNA binding	0.0117724336002034
GO:0045449	regulation of transcription	0.0117724336002034
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0117724336002034
GO:0006350	transcription	0.0117724336002034
GO:0000785	chromatin	0.0117724336002034
GO:0032583	regulation of gene-specific transcription	0.0117724336002034
GO:0010468	regulation of gene expression	0.0122181804073108
GO:0031323	regulation of cellular metabolic process	0.0135249862227857
GO:0019222	regulation of metabolic process	0.0147854056711222
GO:0001837	epithelial to mesenchymal transition	0.0154048542908589
GO:0044427	chromosomal part	0.0216833268507031
GO:0010467	gene expression	0.0277227841110429
GO:0005694	chromosome	0.0277227841110429
GO:0003676	nucleic acid binding	0.0283307318082205
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0345708430066191
GO:0043565	sequence-specific DNA binding	0.0345708430066191
GO:0042054	histone methyltransferase activity	0.0345708430066191
GO:0043232	intracellular non-membrane-bound organelle	0.0345708430066191
GO:0043228	non-membrane-bound organelle	0.0345708430066191
GO:0006479	protein amino acid methylation	0.0345708430066191
GO:0008213	protein amino acid alkylation	0.0345708430066191
GO:0050794	regulation of cellular process	0.0370591123014948
GO:0008170	N-methyltransferase activity	0.0387003362702759
GO:0008276	protein methyltransferase activity	0.0387003362702759
GO:0048762	mesenchymal cell differentiation	0.0432939771660033
GO:0014031	mesenchymal cell development	0.0432939771660033
GO:0043414	biopolymer methylation	0.0454101306158489
GO:0050789	regulation of biological process	0.0462552943785845
GO:0032259	methylation	0.0462552943785845
GO:0006355	regulation of transcription, DNA-dependent	0.0462552943785845
GO:0006351	transcription, DNA-dependent	0.0462552943785845
GO:0032774	RNA biosynthetic process	0.0462552943785845

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	2.82e-09	33
neuronal stem cell	2.82e-09	33
neuroblast	2.82e-09	33
electrically signaling cell	2.82e-09	33
ectodermal cell	3.12e-07	44
neurectodermal cell	3.12e-07	44
neural cell	4.13e-07	43
CNS neuron (sensu Vertebrata)	7.72e-07	23
neuroblast (sensu Vertebrata)	7.72e-07	23

Uber Anatomy

Ontology term	p-value	n
neurectoderm	6.61e-07	64
neural plate	6.61e-07	64
presumptive neural plate	6.61e-07	64
central nervous system	7.09e-07	73
nervous system	9.72e-07	75

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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