MCL coexpression mm9:687

Phase1 CAGE Peaks

	Short description
Mm9::chr10:21139249..21139266,+	p1@uc007eor.1
Mm9::chr10:21139274..21139287,+	p2@uc007eor.1
Mm9::chr13:44292827..44292838,-	p@chr13:44292827..44292838 -
Mm9::chr15:63302448..63302452,-	p@chr15:63302448..63302452 -
Mm9::chr1:125783911..125783934,-	p@chr1:125783911..125783934 -
Mm9::chr3:130815472..130815497,+	p6@Lef1
Mm9::chr4:102786843..102786903,-	p1@Wdr78
Mm9::chr4:122563323..122563339,-	p7@Cap1
Mm9::chr4:147242717..147242731,-	p3@Miip
Mm9::chr9:20447641..20447659,-	p9@Fbxl12

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:0021542	dentate gyrus development	0.0262970470607571
GO:0008301	DNA bending activity	0.036789649505362
GO:0021766	hippocampus development	0.036789649505362
GO:0048341	paraxial mesoderm formation	0.036789649505362
GO:0045843	negative regulation of striated muscle development	0.036789649505362
GO:0048340	paraxial mesoderm morphogenesis	0.036789649505362
GO:0021761	limbic system development	0.036789649505362
GO:0016202	regulation of striated muscle development	0.036789649505362
GO:0048339	paraxial mesoderm development	0.036789649505362
GO:0021543	pallium development	0.036789649505362
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0373162793455809
GO:0006508	proteolysis	0.0373162793455809
GO:0030879	mammary gland development	0.0373162793455809
GO:0030111	regulation of Wnt receptor signaling pathway	0.0373162793455809
GO:0021537	telencephalon development	0.0373162793455809
GO:0001707	mesoderm formation	0.0373162793455809
GO:0048332	mesoderm morphogenesis	0.0373162793455809
GO:0001890	placenta development	0.0373162793455809
GO:0001704	formation of primary germ layer	0.0373162793455809
GO:0001756	somitogenesis	0.0433140977382263
GO:0042475	odontogenesis of dentine-containing teeth	0.0449942592133951
GO:0042476	odontogenesis	0.045330154040783
GO:0000151	ubiquitin ligase complex	0.0456363404987191
GO:0035282	segmentation	0.0459165321860133

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
thymus	1.69e-16	23
neck	1.69e-16	23
respiratory system epithelium	1.69e-16	23
hemolymphoid system gland	1.69e-16	23
pharyngeal epithelium	1.69e-16	23
thymic region	1.69e-16	23
pharyngeal gland	1.69e-16	23
entire pharyngeal arch endoderm	1.69e-16	23
thymus primordium	1.69e-16	23
early pharyngeal endoderm	1.69e-16	23
pharynx	1.38e-15	24
gland of gut	1.38e-15	24
upper respiratory tract	1.38e-15	24
chordate pharynx	1.38e-15	24
pharyngeal arch system	1.38e-15	24
pharyngeal region of foregut	1.38e-15	24
hemopoietic organ	3.07e-15	29
immune organ	3.07e-15	29
gonad	1.91e-13	18
gonad primordium	1.91e-13	18
segment of respiratory tract	2.92e-13	27
external genitalia	2.50e-12	17
indifferent external genitalia	2.50e-12	17
indifferent gonad	2.50e-12	17
mixed endoderm/mesoderm-derived structure	1.27e-11	35
testis	2.77e-11	14
respiratory tract	4.90e-11	41
craniocervical region	8.33e-11	36
respiratory system	1.25e-10	42
male reproductive organ	2.48e-10	15
hemolymphoid system	5.50e-10	48
immune system	5.50e-10	48
hematopoietic system	7.51e-10	45
blood island	7.51e-10	45
male organism	1.68e-09	16
male reproductive system	1.68e-09	16
reproductive structure	2.35e-09	26
reproductive system	2.35e-09	26
reproductive organ	4.27e-09	24
organ segment	4.59e-09	35
mesoderm	8.82e-09	120
mesoderm-derived structure	8.82e-09	120
presumptive mesoderm	8.82e-09	120
anterior region of body	3.65e-08	43
primordium	7.36e-08	134

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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