MCL coexpression mm9:668

Phase1 CAGE Peaks

	Short description
Mm9::chr13:31898767..31898785,+	p4@Foxc1
Mm9::chr13:99124189..99124205,+	p1@Foxd1
Mm9::chr13:99124236..99124243,+	p2@Foxd1
Mm9::chr13:99124729..99124745,+	p@chr13:99124729..99124745 +
Mm9::chr2:165420509..165420580,+	p1@Eya2
Mm9::chr5:137463527..137463538,+	p9@Plod3
Mm9::chr5:38215819..38215823,-	p1@Msx1
Mm9::chr6:72185396..72185413,-	p6@Atoh8
Mm9::chr8:123640063..123640077,+	p1@Foxc2
Mm9::chr8:123640090..123640101,+	p2@Foxc2
Mm9::chr9:98325725..98325749,+	p@chr9:98325725..98325749 +

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:0003007	heart morphogenesis	5.83960470390845e-05
GO:0008301	DNA bending activity	7.15673488729175e-05
GO:0048844	artery morphogenesis	7.15673488729175e-05
GO:0055010	ventricular cardiac muscle morphogenesis	7.15673488729175e-05
GO:0001945	lymph vessel development	7.15673488729175e-05
GO:0048341	paraxial mesoderm formation	7.5383323061609e-05
GO:0055008	cardiac muscle morphogensis	7.5383323061609e-05
GO:0001822	kidney development	7.5383323061609e-05
GO:0046620	regulation of organ growth	7.66010241537851e-05
GO:0001655	urogenital system development	7.66010241537851e-05
GO:0060038	cardiac muscle cell proliferation	7.70303049760186e-05
GO:0048644	muscle morphogenesis	7.70303049760186e-05
GO:0014855	striated muscle cell proliferation	7.70303049760186e-05
GO:0048340	paraxial mesoderm morphogenesis	9.19479537249385e-05
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.000116604844891553
GO:0035265	organ growth	0.000133418602801376
GO:0006366	transcription from RNA polymerase II promoter	0.000133418602801376
GO:0048339	paraxial mesoderm development	0.000133418602801376
GO:0035050	embryonic heart tube development	0.000133418602801376
GO:0033002	muscle cell proliferation	0.000133418602801376
GO:0043565	sequence-specific DNA binding	0.000133418602801376
GO:0048010	vascular endothelial growth factor receptor signaling pathway	0.000147771138511505
GO:0030199	collagen fibril organization	0.000156267844528636
GO:0001974	blood vessel remodeling	0.000156267844528636
GO:0048468	cell development	0.000175048166605948
GO:0043066	negative regulation of apoptosis	0.000198974838792371
GO:0043069	negative regulation of programmed cell death	0.00019941297764676
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.000217977795038277
GO:0007517	muscle development	0.000246504110865134
GO:0007507	heart development	0.000255872021783747
GO:0001707	mesoderm formation	0.000336138365925494
GO:0006915	apoptosis	0.000336138365925494
GO:0012501	programmed cell death	0.000340740012340497
GO:0048332	mesoderm morphogenesis	0.000340740012340497
GO:0001704	formation of primary germ layer	0.000357419631033899
GO:0008219	cell death	0.000365174092335362
GO:0016265	death	0.000365174092335362
GO:0043009	chordate embryonic development	0.000420508607951796
GO:0009792	embryonic development ending in birth or egg hatching	0.000420508607951796
GO:0001657	ureteric bud development	0.000420508607951796
GO:0014032	neural crest cell development	0.000420508607951796
GO:0014033	neural crest cell differentiation	0.000420508607951796
GO:0035150	regulation of tube size	0.000443745652675687
GO:0050880	regulation of blood vessel size	0.000443745652675687
GO:0003018	vascular process in circulatory system	0.000443745652675687
GO:0014031	mesenchymal cell development	0.000560669895248023
GO:0048762	mesenchymal cell differentiation	0.000560669895248023
GO:0007167	enzyme linked receptor protein signaling pathway	0.000606857514252424
GO:0048869	cellular developmental process	0.000654571451121736
GO:0030154	cell differentiation	0.000654571451121736
GO:0003700	transcription factor activity	0.000654571451121736
GO:0001656	metanephros development	0.000676304752546427
GO:0007498	mesoderm development	0.000787634042924461
GO:0007219	Notch signaling pathway	0.000805111373058172
GO:0006355	regulation of transcription, DNA-dependent	0.000841397142485504
GO:0006351	transcription, DNA-dependent	0.00087015276353609
GO:0032774	RNA biosynthetic process	0.00087015276353609
GO:0003677	DNA binding	0.000908457371142443
GO:0030198	extracellular matrix organization and biogenesis	0.00094426955727915
GO:0045449	regulation of transcription	0.00094426955727915
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00102050811980884
GO:0006350	transcription	0.00106294739370639
GO:0007369	gastrulation	0.00106294739370639
GO:0010468	regulation of gene expression	0.00121365013836572
GO:0042981	regulation of apoptosis	0.00121783817363992
GO:0043067	regulation of programmed cell death	0.00123766949604822
GO:0031323	regulation of cellular metabolic process	0.0014057899455575
GO:0048729	tissue morphogenesis	0.00142083030173103
GO:0043010	camera-type eye development	0.00142083030173103
GO:0003702	RNA polymerase II transcription factor activity	0.00143812190857447
GO:0007275	multicellular organismal development	0.00147269513102191
GO:0006916	anti-apoptosis	0.00147269513102191
GO:0032808	lacrimal gland development	0.00149196716771647
GO:0019222	regulation of metabolic process	0.00151457445837975
GO:0009653	anatomical structure morphogenesis	0.00154863928668225
GO:0016070	RNA metabolic process	0.00167038896588936
GO:0009790	embryonic development	0.00174998546026162
GO:0008283	cell proliferation	0.00190301382543278
GO:0001503	ossification	0.00190683017788915
GO:0031214	biomineral formation	0.0019166685748341
GO:0008015	blood circulation	0.0019166685748341
GO:0003013	circulatory system process	0.0019166685748341
GO:0043062	extracellular structure organization and biogenesis	0.00205577104252653
GO:0046849	bone remodeling	0.00217507082587939
GO:0009887	organ morphogenesis	0.00217507082587939
GO:0001654	eye development	0.00218859969867681
GO:0043283	biopolymer metabolic process	0.00221801486610398
GO:0048343	paraxial mesodermal cell fate commitment	0.00241990447998031
GO:0001946	lymphangiogenesis	0.00241990447998031
GO:0048342	paraxial mesodermal cell differentiation	0.00241990447998031
GO:0048513	organ development	0.00251199589922784
GO:0001701	in utero embryonic development	0.00267450316634048
GO:0048771	tissue remodeling	0.00273480680691769
GO:0010467	gene expression	0.00317181018120513
GO:0008475	procollagen-lysine 5-dioxygenase activity	0.00336735473890061
GO:0001710	mesodermal cell fate commitment	0.00336735473890061
GO:0048333	mesodermal cell differentiation	0.00336735473890061
GO:0003676	nucleic acid binding	0.00340510036640844
GO:0007399	nervous system development	0.00350202083618558
GO:0035239	tube morphogenesis	0.0037545139877692
GO:0040008	regulation of growth	0.0037545139877692
GO:0032502	developmental process	0.0037959290179612
GO:0048703	embryonic viscerocranium morphogenesis	0.00422756924733131
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.00441338829450723
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0045199112998873
GO:0048731	system development	0.00479757132385624
GO:0048514	blood vessel morphogenesis	0.0048250074971598
GO:0031490	chromatin DNA binding	0.00503898223525757
GO:0001501	skeletal development	0.00512211383636323
GO:0007420	brain development	0.00530039310425389
GO:0007423	sensory organ development	0.00531788971464045
GO:0048646	anatomical structure formation	0.00531788971464045
GO:0008354	germ cell migration	0.00572541466457373
GO:0048701	embryonic cranial skeleton morphogenesis	0.00572541466457373
GO:0050794	regulation of cellular process	0.00572541466457373
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.00574991485824074
GO:0048598	embryonic morphogenesis	0.00588061462113732
GO:0035295	tube development	0.00588061462113732
GO:0001568	blood vessel development	0.00594593140978722
GO:0001944	vasculature development	0.00606904610846606
GO:0048523	negative regulation of cellular process	0.00643221661462505
GO:0048856	anatomical structure development	0.00741495559696795
GO:0007417	central nervous system development	0.00741495559696795
GO:0043170	macromolecule metabolic process	0.00741495559696795
GO:0045893	positive regulation of transcription, DNA-dependent	0.00758778392991316
GO:0048519	negative regulation of biological process	0.00758778392991316
GO:0050789	regulation of biological process	0.00855235929487186
GO:0048704	embryonic skeletal morphogenesis	0.00927195405056161
GO:0030901	midbrain development	0.00927195405056161
GO:0016477	cell migration	0.00973041177184383
GO:0009888	tissue development	0.0101390133189321
GO:0045941	positive regulation of transcription	0.0101390133189321
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0104863220917352
GO:0035272	exocrine system development	0.0113547456293787
GO:0065007	biological regulation	0.0125701239648157
GO:0009725	response to hormone stimulus	0.0126885163954944
GO:0048706	embryonic skeletal development	0.0126885163954944
GO:0006928	cell motility	0.0127059919028333
GO:0051674	localization of cell	0.0127059919028333
GO:0005634	nucleus	0.0133156809330556
GO:0032501	multicellular organismal process	0.0135623576584384
GO:0001541	ovarian follicle development	0.0137674292428574
GO:0031325	positive regulation of cellular metabolic process	0.0140356843231172
GO:0044238	primary metabolic process	0.0140356843231172
GO:0006022	aminoglycan metabolic process	0.0140356843231172
GO:0030203	glycosaminoglycan metabolic process	0.0140356843231172
GO:0031418	L-ascorbic acid binding	0.0140356843231172
GO:0044237	cellular metabolic process	0.0142132735767427
GO:0043231	intracellular membrane-bound organelle	0.0145660465564809
GO:0043227	membrane-bound organelle	0.0145660465564809
GO:0009893	positive regulation of metabolic process	0.0149727271035296
GO:0001569	patterning of blood vessels	0.0157094986923561
GO:0048705	skeletal morphogenesis	0.0163135424484417
GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	0.0174975588847288
GO:0008286	insulin receptor signaling pathway	0.0174975588847288
GO:0005667	transcription factor complex	0.0184482272073624
GO:0030509	BMP signaling pathway	0.0198986971425132
GO:0022601	menstrual cycle phase	0.0198986971425132
GO:0022602	menstrual cycle process	0.0204520341561944
GO:0008585	female gonad development	0.0236921077603396
GO:0046660	female sex differentiation	0.0240642194559199
GO:0046545	development of primary female sexual characteristics	0.0240642194559199
GO:0009880	embryonic pattern specification	0.0261971158750841
GO:0042698	menstrual cycle	0.0261971158750841
GO:0043229	intracellular organelle	0.0261971158750841
GO:0043226	organelle	0.0261971158750841
GO:0044451	nucleoplasm part	0.0264031601890037
GO:0005654	nucleoplasm	0.028695203783531
GO:0043566	structure-specific DNA binding	0.0306960714670178
GO:0008632	apoptotic program	0.0311461302958456
GO:0008406	gonad development	0.032217241520755
GO:0048608	reproductive structure development	0.0332750766735975
GO:0065008	regulation of biological quality	0.0343796788979883
GO:0045137	development of primary sexual characteristics	0.0357606165460643
GO:0048754	branching morphogenesis of a tube	0.0357606165460643
GO:0051213	dioxygenase activity	0.0359602319518678
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.0359602319518678
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.036358308862171
GO:0031981	nuclear lumen	0.0373187989706492
GO:0001763	morphogenesis of a branching structure	0.0373187989706492
GO:0030326	embryonic limb morphogenesis	0.0373187989706492
GO:0035113	embryonic appendage morphogenesis	0.0373187989706492
GO:0048609	reproductive process in a multicellular organism	0.0415459412171078
GO:0032504	multicellular organism reproduction	0.0415459412171078
GO:0007548	sex differentiation	0.0424714038642085
GO:0048732	gland development	0.0428147060306397
GO:0048522	positive regulation of cellular process	0.0432596892398072
GO:0035107	appendage morphogenesis	0.0432596892398072
GO:0035108	limb morphogenesis	0.0432596892398072
GO:0007165	signal transduction	0.0433399854871231
GO:0043233	organelle lumen	0.0433399854871231
GO:0031974	membrane-enclosed lumen	0.0433399854871231
GO:0060173	limb development	0.0433399854871231
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0433399854871231
GO:0048736	appendage development	0.0433399854871231
GO:0007411	axon guidance	0.0433399854871231
GO:0004725	protein tyrosine phosphatase activity	0.0466500409963091
GO:0003006	reproductive developmental process	0.0466500409963091

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	2.71e-09	92
ecto-epithelium	1.27e-07	73
neurectoderm	3.82e-07	64
neural plate	3.82e-07	64
presumptive neural plate	3.82e-07	64
ectoderm-derived structure	5.04e-07	95
ectoderm	5.04e-07	95
presumptive ectoderm	5.04e-07	95

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)
MA0003.1	1.57537
MA0004.1	0.879856
MA0006.1	0.186435
MA0007.1	0.316976
MA0009.1	0.743257
MA0014.1	0.919317
MA0017.1	0.207884
MA0019.1	0.567591
MA0024.1	0.70077
MA0025.1	0.971686
MA0027.1	2.37948
MA0028.1	0.567414
MA0029.1	0.679737
MA0030.1	0.686088
MA0031.1	0.651724
MA0038.1	0.462726
MA0040.1	0.755433
MA0041.1	0.263922
MA0042.1	0.252679
MA0043.1	0.837621
MA0046.1	0.778239
MA0048.1	1.17627
MA0050.1	0.365212
MA0051.1	0.471092
MA0052.1	0.76328
MA0055.1	1.79839
MA0056.1	0
MA0057.1	0.406124
MA0058.1	1.27846
MA0059.1	2.03293
MA0060.1	0.789184
MA0061.1	0.147394
MA0063.1	0
MA0066.1	0.452472
MA0067.1	1.08124
MA0068.1	0.187364
MA0069.1	0.76361
MA0070.1	2.97928
MA0071.1	0.364454
MA0072.1	0.745922
MA0073.1	0.0672071
MA0074.1	1.07546
MA0076.1	0.223625
MA0077.1	0.724865
MA0078.1	0.502121
MA0081.1	0.277253
MA0083.1	0.836845
MA0084.1	1.4063
MA0087.1	0.794721
MA0088.1	0.534411
MA0089.1	0
MA0090.1	0.299987
MA0091.1	0.342071
MA0092.1	0.812369
MA0093.1	0.58345
MA0095.1	0
MA0098.1	0
MA0100.1	0.408523
MA0101.1	0.265031
MA0103.1	0.216742
MA0105.1	0.0759118
MA0106.1	0.509454
MA0107.1	0.211681
MA0108.2	0.589413
MA0109.1	0
MA0111.1	0.839864
MA0113.1	0.482899
MA0114.1	0.145642
MA0115.1	0.84036
MA0116.1	0.186271
MA0117.1	0.808813
MA0119.1	0.733279
MA0122.1	0.828211
MA0124.1	1.02871
MA0125.1	0.955734
MA0130.1	0
MA0131.1	2.36861
MA0132.1	0
MA0133.1	0
MA0135.1	0.873285
MA0136.1	0.437601
MA0139.1	2.28235
MA0140.1	0.408417
MA0141.1	0.233109
MA0142.1	0.63775
MA0143.1	0.49828
MA0144.1	0.88666
MA0145.1	0.3137
MA0146.1	2.1827
MA0147.1	0.475899
MA0148.1	0.344843
MA0149.1	0.269772
MA0062.2	0.0791588
MA0035.2	0.412747
MA0039.2	0.35217
MA0138.2	0.555696
MA0002.2	0.105469
MA0137.2	0.652494
MA0104.2	0.369356
MA0047.2	0.46201
MA0112.2	0.133279
MA0065.2	0.133827
MA0150.1	0.316876
MA0151.1	0
MA0152.1	1.16826
MA0153.1	0.889592
MA0154.1	0.759699
MA0155.1	0.354827
MA0156.1	0.634231
MA0157.1	0.606944
MA0158.1	0
MA0159.1	0.495113
MA0160.1	0.918217
MA0161.1	0
MA0162.1	1.95903
MA0163.1	0.355774
MA0164.1	0.437937
MA0080.2	0.609443
MA0018.2	0.446948
MA0099.2	0.549696
MA0079.2	2.00278
MA0102.2	1.45844
MA0258.1	0.135621
MA0259.1	0.455671
MA0442.1	0