MCL coexpression mm9:262

Phase1 CAGE Peaks

	Short description
Mm9::chr11:105153425..105153467,+	p4@Mrc2
Mm9::chr12:34642510..34642530,+	p1@Twist1
Mm9::chr14:56443742..56443756,+	p6@Nfatc4
Mm9::chr1:129434016..129434023,-	p5@Tmem163
Mm9::chr1:165288513..165288518,+	p@chr1:165288513..165288518 +
Mm9::chr2:33574246..33574257,-	p3@ENSMUST00000130532
Mm9::chr2:33574267..33574279,-	p1@ENSMUST00000130532
Mm9::chr2:33574309..33574319,-	p4@ENSMUST00000130532
Mm9::chr2:51893662..51893675,+	p2@Tnfaip6
Mm9::chr2:74499251..74499258,-	p4@Evx2
Mm9::chr2:74499300..74499309,-	p5@Evx2
Mm9::chr2:74506264..74506286,+	p1@Hoxd13
Mm9::chr2:74513064..74513089,+	p2@Hoxd12
Mm9::chr2:74513125..74513143,+	p1@Hoxd12
Mm9::chr2:74513149..74513159,+	p@chr2:74513149..74513159 +
Mm9::chr2:74520048..74520064,+	p1@Hoxd11
Mm9::chr2:74521516..74521525,+	p1@ENSMUST00000136302
Mm9::chr3:29912271..29912291,-	p16@Mecom
Mm9::chr3:29912310..29912321,-	p23@Mecom
Mm9::chr3:86116124..86116132,+	p@chr3:86116124..86116132 +
Mm9::chr4:154011072..154011095,-	p6@Prdm16
Mm9::chr4:58566619..58566642,-	p9@Lpar1
Mm9::chr5:120246522..120246553,+	p@chr5:120246522..120246553 +
Mm9::chr5:120246556..120246565,+	p@chr5:120246556..120246565 +
Mm9::chr5:120256413..120256428,-	p@chr5:120256413..120256428 -
Mm9::chr6:30660527..30660538,-	p@chr6:30660527..30660538 -
Mm9::chr6:52185119..52185126,+	p@chr6:52185119..52185126 +
Mm9::chr6:52195000..52195013,+	p3@Hoxa11as
Mm9::chr6:52195023..52195038,+	p1@Hoxa11as
Mm9::chr6:52210774..52210787,-	p1@Hoxa13
Mm9::chr6:52210816..52210831,-	p2@Hoxa13
Mm9::chr9:32350571..32350593,-	p@chr9:32350571..32350593 -

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:0007389	pattern specification process	0.000473097416261886
GO:0003700	transcription factor activity	0.00128291389413705
GO:0005667	transcription factor complex	0.00128291389413705
GO:0043565	sequence-specific DNA binding	0.00128291389413705
GO:0009887	organ morphogenesis	0.00147536142509066
GO:0044451	nucleoplasm part	0.00147536142509066
GO:0001501	skeletal development	0.00147536142509066
GO:0009653	anatomical structure morphogenesis	0.00147536142509066
GO:0005654	nucleoplasm	0.00147536142509066
GO:0031981	nuclear lumen	0.00259470647301078
GO:0048513	organ development	0.00266446791328663
GO:0031974	membrane-enclosed lumen	0.00317368745954419
GO:0043233	organelle lumen	0.00317368745954419
GO:0030326	embryonic limb morphogenesis	0.00415540629745191
GO:0035113	embryonic appendage morphogenesis	0.00415540629745191
GO:0048731	system development	0.00489650441409066
GO:0035107	appendage morphogenesis	0.00489650441409066
GO:0035108	limb morphogenesis	0.00489650441409066
GO:0060173	limb development	0.00489650441409066
GO:0048736	appendage development	0.00489650441409066
GO:0044428	nuclear part	0.00551324171480623
GO:0006355	regulation of transcription, DNA-dependent	0.00551324171480623
GO:0006351	transcription, DNA-dependent	0.00551324171480623
GO:0032774	RNA biosynthetic process	0.00551324171480623
GO:0003677	DNA binding	0.00560995379016853
GO:0045449	regulation of transcription	0.00578422189955604
GO:0048856	anatomical structure development	0.00587999880279197
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00587999880279197
GO:0006350	transcription	0.00602887185361421
GO:0010468	regulation of gene expression	0.0067870812496044
GO:0031323	regulation of cellular metabolic process	0.00790017989892396
GO:0007275	multicellular organismal development	0.00849566317085947
GO:0019222	regulation of metabolic process	0.00876372901634206
GO:0016070	RNA metabolic process	0.00958001881999868
GO:0046332	SMAD binding	0.0139741292509268
GO:0045843	negative regulation of striated muscle development	0.0139741292509268
GO:0005518	collagen binding	0.0139741292509268
GO:0048598	embryonic morphogenesis	0.0162956286286687
GO:0043234	protein complex	0.0180532963462087
GO:0010467	gene expression	0.0183035077001981
GO:0003676	nucleic acid binding	0.0198566542060702
GO:0035115	embryonic forelimb morphogenesis	0.0208469733473235
GO:0032502	developmental process	0.0208469733473235
GO:0016202	regulation of striated muscle development	0.0208469733473235
GO:0010092	specification of organ identity	0.0208469733473235
GO:0001759	induction of an organ	0.0208469733473235
GO:0031128	induction	0.0215104325091062
GO:0045168	cell-cell signaling during cell fate commitment	0.0215104325091062
GO:0030246	carbohydrate binding	0.0216351742869658
GO:0035136	forelimb morphogenesis	0.022120169814977
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0222185820997572
GO:0005540	hyaluronic acid binding	0.0226823841787019
GO:0050794	regulation of cellular process	0.0290204774403076
GO:0032991	macromolecular complex	0.0299126914371503
GO:0035137	hindlimb morphogenesis	0.0307801926670324
GO:0050789	regulation of biological process	0.043652504504262
GO:0044446	intracellular organelle part	0.0481157019908402
GO:0044422	organelle part	0.0481157019908402
GO:0009790	embryonic development	0.0488680045372098

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
forelimb	2.69e-17	7
pectoral appendage	2.69e-17	7
pectoral appendage bud	2.69e-17	7
forelimb bud	2.69e-17	7
forelimb/pectoral fin field	2.69e-17	7
pectoral complex	5.66e-15	8
appendage	1.49e-09	12
paired limb/fin	1.49e-09	12
limb	1.49e-09	12
paired limb/fin bud	1.49e-09	12
limb bud	1.49e-09	12
limb/fin field	1.49e-09	12
limb field	1.49e-09	12
appendage girdle complex	1.01e-08	13
surface structure	3.05e-07	22

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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