MCL coexpression mm9:311

Phase1 CAGE Peaks

	Short description
Mm9::chr11:30549364..30549374,-	p@chr11:30549364..30549374 -
Mm9::chr11:30549375..30549413,-	p1@Acyp2
Mm9::chr11:30549417..30549445,-	p2@Acyp2
Mm9::chr15:97938965..97939006,+	p1@Pfkm
Mm9::chr17:24769553..24769577,-	p1@Tsc2
Mm9::chr17:72131974..72132061,+	p@chr17:72131974..72132061 +
Mm9::chr1:183950388..183950422,-	p2@Enah
Mm9::chr2:71205594..71205618,-	p1@Slc25a12
Mm9::chr4:115457601..115457657,+	p1@Atpaf1
Mm9::chr4:122878659..122878674,+	p3@Nt5c1a
Mm9::chr4:151235807..151235870,-	p1@Camta1
Mm9::chr5:111239099..111239132,-	p2@Ulk1
Mm9::chr5:35399499..35399544,+	p1@Dok7
Mm9::chr5:74038959..74038993,-	p1@Sgcb
Mm9::chr5:89363237..89363264,+	p6@Slc4a4
Mm9::chr6:127059535..127059587,-	p1@9630033F20Rik
Mm9::chr7:112730112..112730128,-	p4@Apbb1
Mm9::chr7:96780993..96781002,+	p12@Me3
Mm9::chr7:96781009..96781052,+	p4@Me3
Mm9::chr8:107800283..107800326,+	p2@Nol3
Mm9::chr8:107800338..107800382,+	p1@Nol3
Mm9::chr8:13287814..13287856,-	p1@Dcun1d2
Mm9::chr8:7002766..7002788,-	p@chr8:7002766..7002788 -
Mm9::chr8:75095912..75095923,+	p3@Tmem38a
Mm9::chr8:75095968..75096013,+	p2@Tmem38a
Mm9::chr9:122714642..122714698,+	p1@D9Ertd402e

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:0032990	cell part morphogenesis	0.0191122493797354
GO:0048858	cell projection morphogenesis	0.0191122493797354
GO:0030030	cell projection organization and biogenesis	0.0191122493797354
GO:0045792	negative regulation of cell size	0.0191277037517963
GO:0043112	receptor metabolic process	0.021094805142216
GO:0016528	sarcoplasm	0.021094805142216
GO:0007409	axonogenesis	0.021094805142216
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.021094805142216
GO:0048667	neuron morphogenesis during differentiation	0.021094805142216
GO:0048812	neurite morphogenesis	0.021094805142216
GO:0000904	cellular morphogenesis during differentiation	0.021094805142216
GO:0001843	neural tube closure	0.021094805142216
GO:0031175	neurite development	0.021094805142216
GO:0014020	primary neural tube formation	0.021094805142216
GO:0032989	cellular structure morphogenesis	0.021094805142216
GO:0000902	cell morphogenesis	0.021094805142216
GO:0021933	radial glia guided migration of granule cell	0.021094805142216
GO:0050757	thymidylate synthase biosynthetic process	0.021094805142216
GO:0008510	sodium:bicarbonate symporter activity	0.021094805142216
GO:0050760	negative regulation of thymidylate synthase biosynthetic process	0.021094805142216
GO:0051386	regulation of nerve growth factor receptor signaling pathway	0.021094805142216
GO:0050758	regulation of thymidylate synthase biosynthetic process	0.021094805142216
GO:0014067	negative regulation of phosphoinositide 3-kinase cascade	0.021094805142216
GO:0048666	neuron development	0.0246203393221278
GO:0001841	neural tube formation	0.0246703249895695
GO:0001839	neural plate morphogenesis	0.0246703249895695
GO:0001840	neural plate development	0.0246703249895695
GO:0001838	embryonic epithelial tube formation	0.0246703249895695
GO:0016044	membrane organization and biogenesis	0.0246703249895695
GO:0021915	neural tube development	0.0262137604618714
GO:0021932	hindbrain radial glia guided cell migration	0.0262137604618714
GO:0043490	malate-aspartate shuttle	0.0262137604618714
GO:0048670	regulation of collateral sprouting	0.0262137604618714
GO:0043547	positive regulation of GTPase activity	0.0262137604618714
GO:0014066	regulation of phosphoinositide 3-kinase cascade	0.0262137604618714
GO:0003998	acylphosphatase activity	0.0262137604618714
GO:0048671	negative regulation of collateral sprouting	0.0262137604618714
GO:0007167	enzyme linked receptor protein signaling pathway	0.0274931504544667
GO:0016477	cell migration	0.0284840120622137
GO:0016331	morphogenesis of embryonic epithelium	0.0284840120622137
GO:0030182	neuron differentiation	0.0285935180172963
GO:0007411	axon guidance	0.0290837250523788
GO:0007399	nervous system development	0.0290837250523788
GO:0014065	phosphoinositide 3-kinase cascade	0.0290837250523788
GO:0005945	6-phosphofructokinase complex	0.0290837250523788
GO:0048668	collateral sprouting	0.0290837250523788
GO:0035035	histone acetyltransferase binding	0.0290837250523788
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.0290837250523788
GO:0004473	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity	0.0290837250523788
GO:0021535	cell migration in hindbrain	0.0290837250523788
GO:0048699	generation of neurons	0.0307620993761674
GO:0048468	cell development	0.0307620993761674
GO:0006928	cell motility	0.0307620993761674
GO:0051674	localization of cell	0.0307620993761674
GO:0031623	receptor internalization	0.0307620993761674
GO:0004470	malic enzyme activity	0.0307620993761674
GO:0021684	cerebellar granular layer formation	0.0307620993761674
GO:0051898	negative regulation of protein kinase B signaling cascade	0.0307620993761674
GO:0021683	cerebellar granular layer morphogenesis	0.0307620993761674
GO:0003872	6-phosphofructokinase activity	0.0307620993761674
GO:0015701	bicarbonate transport	0.0307620993761674
GO:0021681	cerebellar granular layer development	0.0307620993761674
GO:0021707	cerebellar granule cell differentiation	0.0307620993761674
GO:0006810	transport	0.031108361863902
GO:0022008	neurogenesis	0.0313862890906252
GO:0043062	extracellular structure organization and biogenesis	0.0313862890906252
GO:0051234	establishment of localization	0.0327214534708273
GO:0008361	regulation of cell size	0.0327214534708273
GO:0006108	malate metabolic process	0.0327214534708273
GO:0051896	regulation of protein kinase B signaling cascade	0.0327214534708273
GO:0046626	regulation of insulin receptor signaling pathway	0.0327214534708273
GO:0033261	regulation of progression through S phase	0.0327214534708273
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0327214534708273
GO:0007090	regulation of S phase of mitotic cell cycle	0.0327214534708273
GO:0045786	negative regulation of progression through cell cycle	0.0372347761055763
GO:0016012	sarcoglycan complex	0.0372347761055763
GO:0048011	nerve growth factor receptor signaling pathway	0.0372347761055763
GO:0005522	profilin binding	0.0372347761055763
GO:0002009	morphogenesis of an epithelium	0.0399934514235954
GO:0051320	S phase	0.0408046698041314
GO:0001540	beta-amyloid binding	0.0408046698041314
GO:0000084	S phase of mitotic cell cycle	0.0408046698041314
GO:0016011	dystroglycan complex	0.0408046698041314
GO:0016615	malate dehydrogenase activity	0.0439637854989046
GO:0050821	protein stabilization	0.0439637854989046
GO:0050918	positive chemotaxis	0.0439637854989046
GO:0008253	5'-nucleotidase activity	0.0439637854989046
GO:0005452	inorganic anion exchanger activity	0.0439637854989046
GO:0008252	nucleotidase activity	0.0467783819454978
GO:0008443	phosphofructokinase activity	0.0467783819454978
GO:0031647	regulation of protein stability	0.0467783819454978
GO:0043648	dicarboxylic acid metabolic process	0.0467783819454978
GO:0048009	insulin-like growth factor receptor signaling pathway	0.0467783819454978
GO:0007010	cytoskeleton organization and biogenesis	0.0473879024900326
GO:0035239	tube morphogenesis	0.0474167201603526
GO:0051179	localization	0.0474167201603526
GO:0015380	anion exchanger activity	0.0493011957011837
GO:0017124	SH3 domain binding	0.0493011957011837

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
structure with developmental contribution from neural crest	2.76e-22	92
ectoderm-derived structure	6.26e-17	95
ectoderm	6.26e-17	95
presumptive ectoderm	6.26e-17	95
central nervous system	2.79e-16	73
nervous system	3.81e-16	75
regional part of nervous system	6.29e-15	54
neurectoderm	3.72e-14	64
neural plate	3.72e-14	64
presumptive neural plate	3.72e-14	64
neural tube	8.37e-14	52
neural rod	8.37e-14	52
future spinal cord	8.37e-14	52
neural keel	8.37e-14	52
ecto-epithelium	1.29e-13	73
brain	1.06e-11	47
future brain	1.06e-11	47
anatomical conduit	2.93e-11	122
regional part of brain	3.39e-11	46
tube	1.38e-10	114
gray matter	3.24e-10	34
pre-chordal neural plate	6.63e-10	49
anterior neural tube	3.20e-09	40
regional part of forebrain	1.06e-08	39
forebrain	1.06e-08	39
future forebrain	1.06e-08	39
brain grey matter	2.74e-08	29
regional part of telencephalon	2.74e-08	29
telencephalon	2.74e-08	29
compound organ	1.06e-07	43
multi-cellular organism	1.10e-07	333
primary circulatory organ	2.44e-07	18
heart	2.44e-07	18
primitive heart tube	2.44e-07	18
primary heart field	2.44e-07	18
anterior lateral plate mesoderm	2.44e-07	18
heart tube	2.44e-07	18
heart primordium	2.44e-07	18
cardiac mesoderm	2.44e-07	18
cardiogenic plate	2.44e-07	18
heart rudiment	2.44e-07	18
tissue	2.80e-07	349
regional part of cerebral cortex	7.72e-07	17

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)
{{{tfbs_overrepresentation_jaspar}}}