MCL coexpression mm9:932

Phase1 CAGE Peaks

	Short description
Mm9::chr12:25257265..25257294,+	p2@Grhl1
Mm9::chr12:25257298..25257323,+	p5@Grhl1
Mm9::chr12:25257443..25257454,+	p@chr12:25257443..25257454 +
Mm9::chr13:40826961..40827001,-	p4@Tfap2a
Mm9::chr13:40827030..40827039,-	p12@Tfap2a
Mm9::chr16:25802129..25802142,+	p3@Trp63
Mm9::chr1:162180221..162180250,-	p@chr1:162180221..162180250 -
Mm9::chr1:52784099..52784112,-	p5@Mfsd6

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:0060157	urinary bladder development	0.00712211691228839
GO:0007499	ectoderm and mesoderm interaction	0.00712211691228839
GO:0048745	smooth muscle development	0.0128170009285442
GO:0030859	polarized epithelial cell differentiation	0.0128170009285442
GO:0001736	establishment of planar polarity	0.0128170009285442
GO:0007164	establishment of tissue polarity	0.0128170009285442
GO:0002347	response to tumor cell	0.0128170009285442
GO:0010464	regulation of mesenchymal cell proliferation	0.0128170009285442
GO:0002053	positive regulation of mesenchymal cell proliferation	0.0128170009285442
GO:0010463	mesenchymal cell proliferation	0.0128170009285442
GO:0001738	morphogenesis of a polarized epithelium	0.0142403317223895
GO:0030308	negative regulation of cell growth	0.0153344811757127
GO:0031069	hair follicle morphogenesis	0.0153344811757127
GO:0003700	transcription factor activity	0.0179945999811227
GO:0045792	negative regulation of cell size	0.0180337993848102
GO:0030216	keratinocyte differentiation	0.0204637457246617
GO:0045926	negative regulation of growth	0.0209336305578342
GO:0042475	odontogenesis of dentine-containing teeth	0.0244718933920709
GO:0030855	epithelial cell differentiation	0.0244718933920709
GO:0042476	odontogenesis	0.0244718933920709
GO:0022404	molting cycle process	0.0244718933920709
GO:0001942	hair follicle development	0.0244718933920709
GO:0022405	hair cycle process	0.0244718933920709
GO:0042633	hair cycle	0.0244718933920709
GO:0042303	molting cycle	0.0244718933920709
GO:0007498	mesoderm development	0.0254019884354623
GO:0048730	epidermis morphogenesis	0.0254019884354623
GO:0007219	Notch signaling pathway	0.0254019884354623
GO:0048729	tissue morphogenesis	0.0339951142558933
GO:0006916	anti-apoptosis	0.0339951142558933
GO:0001655	urogenital system development	0.0339951142558933
GO:0001558	regulation of cell growth	0.0339951142558933
GO:0006355	regulation of transcription, DNA-dependent	0.0339951142558933
GO:0006351	transcription, DNA-dependent	0.0339951142558933
GO:0032774	RNA biosynthetic process	0.0339951142558933
GO:0003677	DNA binding	0.0339951142558933
GO:0016049	cell growth	0.0339951142558933
GO:0008544	epidermis development	0.0339951142558933
GO:0045449	regulation of transcription	0.0339951142558933
GO:0003682	chromatin binding	0.0339951142558933
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0339951142558933
GO:0007398	ectoderm development	0.0339951142558933
GO:0006350	transcription	0.0339951142558933
GO:0008361	regulation of cell size	0.0345388012483832
GO:0010468	regulation of gene expression	0.0347026954525265
GO:0045786	negative regulation of progression through cell cycle	0.0352127502353597
GO:0031323	regulation of cellular metabolic process	0.0352127502353597
GO:0002009	morphogenesis of an epithelium	0.0352127502353597
GO:0007275	multicellular organismal development	0.0352127502353597
GO:0019222	regulation of metabolic process	0.0352127502353597
GO:0006917	induction of apoptosis	0.0352127502353597
GO:0012502	induction of programmed cell death	0.0352127502353597
GO:0016070	RNA metabolic process	0.0361708086362291
GO:0040008	regulation of growth	0.0382507329653004
GO:0043066	negative regulation of apoptosis	0.0382507329653004
GO:0043069	negative regulation of programmed cell death	0.0382507329653004
GO:0043065	positive regulation of apoptosis	0.0398958467286218
GO:0043068	positive regulation of programmed cell death	0.0398958467286218
GO:0007517	muscle development	0.0398958467286218
GO:0008284	positive regulation of cell proliferation	0.0411514437931659
GO:0000074	regulation of progression through cell cycle	0.0411514437931659
GO:0001501	skeletal development	0.0411514437931659
GO:0010467	gene expression	0.0435781569476487
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.043610113538687
GO:0003676	nucleic acid binding	0.0443000978803313
GO:0009607	response to biotic stimulus	0.044849721980422
GO:0032502	developmental process	0.0457746405621668
GO:0007389	pattern specification process	0.0477743066906491
GO:0045893	positive regulation of transcription, DNA-dependent	0.0477743066906491
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0477743066906491

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
surface structure	6.09e-10	22
zone of skin	2.97e-07	5
skin epidermis	2.97e-07	5
skin of body	2.97e-07	5
integument	2.97e-07	5
surface	2.97e-07	5
outer epithelium	2.97e-07	5
integumental system	2.97e-07	5
enveloping layer of ectoderm	2.97e-07	5
orifice	3.40e-07	5

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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