MCL coexpression mm9:813

Phase1 CAGE Peaks

	Short description
Mm9::chr13:104968878..104968952,+	p1@Trim23
Mm9::chr17:32487480..32487513,-	p1@Akap8l
Mm9::chr3:151856767..151856795,-	p5@Dnajb4
Mm9::chr3:154756157..154756204,-	p@chr3:154756157..154756204 -
Mm9::chr5:110352652..110352683,+	p1@ENSMUST00000112544
Mm9::chr7:28516392..28516416,+	p2@Zfp60
Mm9::chr7:48888915..48888973,+	p1@Zfp788
Mm9::chr8:93837122..93837178,-	p1@Rpgrip1l
Mm9::chr9:59201237..59201272,-	p1@Bbs4

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:0042384	cilium biogenesis	0.00181597261659763
GO:0005813	centrosome	0.00521245039954293
GO:0030031	cell projection biogenesis	0.00521245039954293
GO:0005815	microtubule organizing center	0.00521245039954293
GO:0021915	neural tube development	0.00521245039954293
GO:0007380	specification of segmental identity, head	0.00521245039954293
GO:0031344	regulation of cell projection organization and biogenesis	0.00521245039954293
GO:0007382	specification of segmental identity, maxillary segment	0.00521245039954293
GO:0035287	head segmentation	0.00521245039954293
GO:0022038	corpus callosum development	0.00521245039954293
GO:0042305	specification of segmental identity, mandibular segment	0.00521245039954293
GO:0030092	regulation of flagellum biogenesis	0.00521245039954293
GO:0035289	posterior head segmentation	0.00521245039954293
GO:0045724	positive regulation of flagellum biogenesis	0.00521245039954293
GO:0001654	eye development	0.00703231761823199
GO:0021670	lateral ventricle development	0.00810714557875194
GO:0060039	pericardium development	0.00810714557875194
GO:0021591	ventricular system development	0.00810714557875194
GO:0021988	olfactory lobe development	0.010943147442655
GO:0021772	olfactory bulb development	0.010943147442655
GO:0035085	cilium axoneme	0.012685969360038
GO:0043584	nose development	0.012685969360038
GO:0001895	retinal homeostasis	0.012685969360038
GO:0007423	sensory organ development	0.0139499293895927
GO:0035058	sensory cilium biogenesis	0.0140258332338738
GO:0046548	retinal rod cell development	0.0140258332338738
GO:0048598	embryonic morphogenesis	0.0144545584929123
GO:0051130	positive regulation of cellular component organization and biogenesis	0.014584868654392
GO:0007350	blastoderm segmentation	0.014584868654392
GO:0009296	flagellum biogenesis	0.014584868654392
GO:0043009	chordate embryonic development	0.0151035449562389
GO:0009792	embryonic development ending in birth or egg hatching	0.0151035449562389
GO:0043064	flagellum organization and biogenesis	0.0154666814034071
GO:0021532	neural tube patterning	0.0166638556714407
GO:0007379	segment specification	0.0166638556714407
GO:0005932	basal body	0.0175089628525996
GO:0032990	cell part morphogenesis	0.0175089628525996
GO:0048858	cell projection morphogenesis	0.0175089628525996
GO:0030030	cell projection organization and biogenesis	0.0175089628525996
GO:0045494	photoreceptor cell maintenance	0.0182210999226393
GO:0015630	microtubule cytoskeleton	0.0190610103069554
GO:0008589	regulation of smoothened signaling pathway	0.0203342613919625
GO:0035115	embryonic forelimb morphogenesis	0.0203342613919625
GO:0044441	cilium part	0.0221700589639689
GO:0035116	embryonic hindlimb morphogenesis	0.0221700589639689
GO:0042462	eye photoreceptor cell development	0.0221700589639689
GO:0035136	forelimb morphogenesis	0.0232450541616362
GO:0001754	eye photoreceptor cell differentiation	0.0242748426948801
GO:0042461	photoreceptor cell development	0.0252621924078737
GO:0019216	regulation of lipid metabolic process	0.0276619525470583
GO:0001889	liver development	0.0293571774882767
GO:0046530	photoreceptor cell differentiation	0.0293571774882767
GO:0005930	axoneme	0.0293571774882767
GO:0035137	hindlimb morphogenesis	0.0293571774882767
GO:0022037	metencephalon development	0.0293571774882767
GO:0021549	cerebellum development	0.0293571774882767
GO:0021537	telencephalon development	0.0293571774882767
GO:0001894	tissue homeostasis	0.0305940695014491
GO:0009790	embryonic development	0.0305940695014491
GO:0048871	multicellular organismal homeostasis	0.0305940695014491
GO:0043232	intracellular non-membrane-bound organelle	0.0305940695014491
GO:0043228	non-membrane-bound organelle	0.0305940695014491
GO:0000902	cell morphogenesis	0.0308300686697638
GO:0032989	cellular structure morphogenesis	0.0308300686697638
GO:0007224	smoothened signaling pathway	0.031319052062797
GO:0009887	organ morphogenesis	0.0348488304909991
GO:0007368	determination of left/right symmetry	0.0363176403676828
GO:0044430	cytoskeletal part	0.0363176403676828
GO:0009799	determination of symmetry	0.0363176403676828
GO:0009855	determination of bilateral symmetry	0.0363176403676828
GO:0016358	dendrite development	0.0398764047791684
GO:0009880	embryonic pattern specification	0.0403253145120023
GO:0030902	hindbrain development	0.0405181487833023
GO:0007286	spermatid development	0.0405181487833023
GO:0035282	segmentation	0.0405181487833023
GO:0001843	neural tube closure	0.0405181487833023
GO:0048592	eye morphogenesis	0.0405181487833023
GO:0048515	spermatid differentiation	0.0409232834134139
GO:0014020	primary neural tube formation	0.0413179107994317
GO:0031072	heat shock protein binding	0.0429758044872341
GO:0007399	nervous system development	0.0429758044872341
GO:0008270	zinc ion binding	0.0434286716614663
GO:0051128	regulation of cellular component organization and biogenesis	0.0465727875817791
GO:0001841	neural tube formation	0.0465727875817791
GO:0001839	neural plate morphogenesis	0.0468707672082345
GO:0001840	neural plate development	0.0474454949779165
GO:0001838	embryonic epithelial tube formation	0.0474454949779165
GO:0051082	unfolded protein binding	0.0477227257535389
GO:0030534	adult behavior	0.0496068184300374

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
neurectoderm	2.23e-13	64
neural plate	2.23e-13	64
presumptive neural plate	2.23e-13	64
ecto-epithelium	6.90e-13	73
structure with developmental contribution from neural crest	7.58e-12	92
pre-chordal neural plate	2.19e-11	49
ectoderm-derived structure	1.36e-10	95
ectoderm	1.36e-10	95
presumptive ectoderm	1.36e-10	95
regional part of nervous system	7.82e-10	54
neural tube	4.67e-09	52
neural rod	4.67e-09	52
future spinal cord	4.67e-09	52
neural keel	4.67e-09	52
brain	1.06e-08	47
future brain	1.06e-08	47
nervous system	2.59e-08	75
central nervous system	2.64e-08	73
regional part of brain	3.53e-08	46
anterior neural tube	9.73e-08	40
occipital lobe	1.12e-07	10
visual cortex	1.12e-07	10
neocortex	1.12e-07	10
regional part of forebrain	3.29e-07	39
forebrain	3.29e-07	39
future forebrain	3.29e-07	39
multi-cellular organism	3.84e-07	333

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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