MCL coexpression mm9:449

Phase1 CAGE Peaks

	Short description
Mm9::chr10:106920848..106920852,-	p@chr10:106920848..106920852 -
Mm9::chr10:106923133..106923146,-	p1@Myf5
Mm9::chr12:74140323..74140332,+	p1@uc007nvz.1
Mm9::chr15:76993525..76993544,-	p@chr15:76993525..76993544 -
Mm9::chr15:76993546..76993607,-	p@chr15:76993546..76993607 -
Mm9::chr17:45738994..45739005,-	p1@Gm7325
Mm9::chr17:45739019..45739035,-	p3@Gm7325
Mm9::chr17:45739045..45739057,-	p2@Gm7325
Mm9::chr1:136186574..136186592,+	p1@Myog
Mm9::chr1:136186599..136186608,+	p3@Myog
Mm9::chr2:26927548..26927562,-	p4@Tmem8c
Mm9::chr2:26927603..26927613,-	p5@Tmem8c
Mm9::chr7:53631818..53631829,+	p2@Myod1
Mm9::chr7:53631837..53631850,+	p1@Myod1
Mm9::chr8:15060282..15060301,+	p6@Myom2
Mm9::chr8:81337088..81337099,-	p5@Lsm6

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:0003705	RNA polymerase II transcription factor activity, enhancer binding	1.30825649872795e-06
GO:0007517	muscle development	2.24385378621871e-06
GO:0003702	RNA polymerase II transcription factor activity	3.14894467472946e-05
GO:0007519	skeletal muscle development	4.64273339264029e-05
GO:0014706	striated muscle development	7.90474854121923e-05
GO:0048741	skeletal muscle fiber development	0.00221721181591798
GO:0048747	muscle fiber development	0.00221721181591798
GO:0048513	organ development	0.00221721181591798
GO:0048625	myoblast cell fate commitment	0.00369210929248125
GO:0007518	myoblast cell fate determination	0.00369210929248125
GO:0048731	system development	0.00369210929248125
GO:0048856	anatomical structure development	0.00617794943570449
GO:0003700	transcription factor activity	0.00822184566576725
GO:0007275	multicellular organismal development	0.00822184566576725
GO:0016070	RNA metabolic process	0.00895309312046242
GO:0001952	regulation of cell-matrix adhesion	0.0157891795918016
GO:0010467	gene expression	0.0157891795918016
GO:0003676	nucleic acid binding	0.0157891795918016
GO:0008307	structural constituent of muscle	0.0157891795918016
GO:0032502	developmental process	0.0167022049410475
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0187434878481659
GO:0048704	embryonic skeletal morphogenesis	0.0187434878481659
GO:0032982	myosin filament	0.0203009953927489
GO:0005863	striated muscle thick filament	0.0203009953927489
GO:0005859	muscle myosin complex	0.0209858061922863
GO:0016460	myosin II complex	0.0222023357894868
GO:0048706	embryonic skeletal development	0.0222023357894868
GO:0048705	skeletal morphogenesis	0.0286850449302073
GO:0001709	cell fate determination	0.0286850449302073
GO:0048869	cellular developmental process	0.0286850449302073
GO:0030154	cell differentiation	0.0286850449302073
GO:0006402	mRNA catabolic process	0.0286850449302073
GO:0006941	striated muscle contraction	0.0286850449302073
GO:0006355	regulation of transcription, DNA-dependent	0.0286850449302073
GO:0043229	intracellular organelle	0.0286850449302073
GO:0006351	transcription, DNA-dependent	0.0286850449302073
GO:0043226	organelle	0.0286850449302073
GO:0032774	RNA biosynthetic process	0.0286850449302073
GO:0006401	RNA catabolic process	0.0286850449302073
GO:0003677	DNA binding	0.0286850449302073
GO:0005634	nucleus	0.0286850449302073
GO:0001756	somitogenesis	0.0286850449302073
GO:0032501	multicellular organismal process	0.0286850449302073
GO:0045449	regulation of transcription	0.0286850449302073
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0288343685554405
GO:0045445	myoblast differentiation	0.0288343685554405
GO:0043283	biopolymer metabolic process	0.0288343685554405
GO:0006350	transcription	0.0288343685554405
GO:0032991	macromolecular complex	0.0293743797132572
GO:0010468	regulation of gene expression	0.0303893002783488
GO:0035282	segmentation	0.0307669318902937
GO:0030155	regulation of cell adhesion	0.0321065380895143
GO:0031323	regulation of cellular metabolic process	0.0321065380895143
GO:0019222	regulation of metabolic process	0.0348980828944188
GO:0030198	extracellular matrix organization and biogenesis	0.0379645308585611
GO:0016459	myosin complex	0.0379645308585611
GO:0046982	protein heterodimerization activity	0.0392486596754975
GO:0042692	muscle cell differentiation	0.0398010198410609
GO:0007160	cell-matrix adhesion	0.0398010198410609
GO:0030017	sarcomere	0.0409223218011252
GO:0031589	cell-substrate adhesion	0.0409223218011252
GO:0044449	contractile fiber part	0.0414550571125855
GO:0030016	myofibril	0.0440876304488212
GO:0044424	intracellular part	0.0440876304488212
GO:0043292	contractile fiber	0.0440876304488212
GO:0003012	muscle system process	0.0460741289802003
GO:0006936	muscle contraction	0.0460741289802003
GO:0005200	structural constituent of cytoskeleton	0.0481049369305937
GO:0005622	intracellular	0.0490378524892453
GO:0009952	anterior/posterior pattern formation	0.0498838723759717

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
appendage	3.27e-09	12
paired limb/fin	3.27e-09	12
limb	3.27e-09	12
paired limb/fin bud	3.27e-09	12
limb bud	3.27e-09	12
limb/fin field	3.27e-09	12
limb field	3.27e-09	12
surface structure	5.06e-09	22
appendage girdle complex	3.02e-08	13
forelimb	7.15e-07	7
pectoral appendage	7.15e-07	7
pectoral appendage bud	7.15e-07	7
forelimb bud	7.15e-07	7
forelimb/pectoral fin field	7.15e-07	7

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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