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MCL coexpression mm9:2701: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0,0.0866693549214347,0.054287588763892,0.114788046983797,0.200881038511243,0,0.055498933850192,0,0,0,0,0,0,0,0,0,0,0.0212025644513176,0.0372027814322557,0,0.0674512431503735,0,0,0.0214850507912259,0.0298988291256234,0.065689575438576,0,0.05187405740423,0.0251851694391322,0,0.0289918065944652,0,0,0,0.102742746314924,0,0,0.0506130080785807,0,0.060949742349986,0,0,0,0.0171661972418973,0.0267255867465159,0,0,0,0,0.098313277597615,0.0189665594956963,0,0.0224540007379827,0,0,0,0,0.060201751373516,0.0266729310181638,0,0,0,0,0,0,0,0.0379365798684957,0.0470681960614343,0,0,0,0,0,0,0,0,0.107486292845058,0,0,0.0179342662264069,0.0126729411860208,0,0.035644226259987,0,0,0,0,0,0.0105672478608157,0.0105464367459272,0.066194194867847,0.089870634893658,0.199401107833944,0.105979790939108,0.278520991743112,0.170187676589325,0.150014309859332,0,0,0,0,0,0,0,0.052080253340767,0.059344158508384,0.059229270497327,0.114809629811658,0,0.0376337418065127,0,0.0384775301049317,0.0901223798974778,0.0540056129920547,0.0558073840278103,0.0463112896583047,0.481894440789423,0,0,0.0217063266948359,0,0.0572299897922243,0.88081597628606,0.130541259988255,0.103722462254014,0.0329339538696473,0,0,0,0.0202062562254905,0,0.0171350182668475,0,0,0,0,0.0635075672826347,0.0169745097646989,0.0652366449325958,0.174920763309301,0,0,0.0239682911137084,0.0743215931953984,0.018468745945857,0,0,0.240334623901531,0,0,0.0234630905383716,0,0.0640119890914407,0.169571799404169,0.528779969341037,0,0,0,0,0,0,0,0,0,0,0,0.034404294799217,0,0,0.0220051525142016,0.0112844458274858,0.0197534664523989,0,0,0,0,0.187166975129293,0.084555156269182,0,0.0302313764762313,0.0175476516793332,0,0,0,0,0.0220712285691766,0,0.0262678054601152,0,0,0.20199530092783,0.297283027395283,0,0,0,0,0,0.0276438638516919,0.0088766307709278,0.0199314599765119,0,0.0168444410470322,0.162622967264915,0,0,0.0293624003965279,0,0,0,0,0.0217522219232226,0,0,0,0,0.118221428571836,0.105769258102689,0.177678906524118,0.20561954214483,0,0,0,0,0,0,0.0735049267911779,0.123808401131706,0.106163384077617,0.0928399119514605,0.407638449577669,0.10293373789018,0.165251635763347,0,0,0.057900067270923,0.0988951533728683,0.0215546922317108,0.0556588285313127,0,0.0325892178866794,0,0,0,0,0.0291183197118858,0,0,0,0,0,0.109834593917356,0,0,0.153864728178968,0,0,0,0.0250125273252447,0,0,0.0332761579806391,0,0.105287926752698,0,0,0,0,0,0,0,0.0236339951876586,0,0,0,0,0.263002745966233,0,1.14881551644836,1.19117440766728,0.795079559329233,0.796295466255539,0.818645281434784,0.066490133277276,0.0640288646130883,0.0228363351212467,0.0271622003567789,0,0,0,0,0,0.0189621187387963,0,0.627440092923386,0,0,0.0283124632898976,0.250899495677208,0.237161698637686,0.512402914135264,0.516840687582629,0.832353728955286,0.181102564246875,0.139915942196074,0,0,0,0,0,0,0,0,0,0,0,0.0397531863973687,0,0,0.0334386535022533,0,0,0.0164312680455674,0,0,0.0298059097072022,0.0139062504973587,0.0134626204920181,0.0132981630510481,0.0160017698361234,1.19819963036692,0.0290220712522073,0.0248749822295632,0.0643771246096118,0,0.210998021783283,0.13061814941032,0.846408122210925,0,0,0,0.065566624548113,0.0229577345845564,0,0,0,0.0538213987540727,0,0,0.0142951371858648,0,0,0.0315028043834892,0,0.104229130641792,0.0581059221629598,0,0.169399029339407,0.0816805025447873,0.0327057221205027,0.111257277847679,0.148557916555877,0.104058086489886,0.0869436018387511,0.056390921288728,0.0749388100186848,0.0766073954291401,0.0499537055884833,0.105895865118202,0.118274645592862,0.115603705994629,0.0564476561664613,0.103286898892702,0.120632609616948,0.153159077510617,0.0694543997599358,0.0611980703630433,0.147067176615957,0.108934537031869,0.145239698086072,0.127003340049074,0.0865680835831363,0.0599292171909774,0.218180417615648,0.0645627973706778,0.327253073814062,0.595249735933326,0.395314740249433,0.220572027003917,0.0551542189060567|coexpression_dpi_cluster_scores_median=0,0.130004032382152,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0558041721483835,0,0.0682179984609265,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110202921672641,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.225301871178984,0,0,0,0.152695919012311,0,0,0,0,0,0,0,0,0,0,0.0893284091371433,0,0,0,0,0.0901223798974778,0,0,0,0.598389897377065,0,0,0,0,0,0.674662332002395,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421182837367051,0,0.0978549673988937,0.21254064290909,0,0,0,0.0609639314262262,0,0,0,0.360501935852296,0,0,0,0,0,0.12977112683364,0.653048060579305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0849828766602549,0.145594936782439,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191523550257637,0,0,0,0,0,0,0.0774164737207147,0.119015009568782,0.159245076116426,0.0642538110976656,0.331840783439576,0,0.0586723554240733,0,0,0,0.10582914506561,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0663147875126409,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.266544079535733,0,1.01697138183893,1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axon cargo transport;0.00704385189127424;83431!GO:0047496;vesicle transport along microtubule;0.00704385189127424;83431!GO:0001833;inner cell mass cell proliferation;0.00704385189127424;83431!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.00704385189127424;83431!GO:0060053;neurofilament cytoskeleton;0.00704385189127424;83431!GO:0021955;central nervous system neuron axonogenesis;0.00704385189127424;83431!GO:0008088;axon cargo transport;0.00704385189127424;83431!GO:0001832;blastocyst growth;0.00801238152632444;83431!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.00931353750068482;83431!GO:0045103;intermediate filament-based process;0.00941314752743011;83431!GO:0021954;central nervous system neuron development;0.00941314752743011;83431!GO:0021953;central nervous system neuron differentiation;0.00986139264778393;83431!GO:0001824;blastocyst development;0.0117578143108193;83431!GO:0005813;centrosome;0.0142730683060031;83431!GO:0008017;microtubule binding;0.0142730683060031;83431!GO:0048589;developmental growth;0.0142730683060031;83431!GO:0005815;microtubule organizing center;0.0142730683060031;83431!GO:0015631;tubulin binding;0.0142730683060031;83431!GO:0001764;neuron migration;0.0142730683060031;83431!GO:0030424;axon;0.0150268840347184;83431!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0150268840347184;83431!GO:0007018;microtubule-based movement;0.0186021724946833;83431!GO:0030705;cytoskeleton-dependent intracellular transport;0.0209554593765408;83431!GO:0005875;microtubule associated complex;0.0209554593765408;83431!GO:0043005;neuron projection;0.0220968242663307;83431!GO:0001701;in utero embryonic development;0.0220968242663307;83431!GO:0045111;intermediate filament cytoskeleton;0.0220968242663307;83431!GO:0007409;axonogenesis;0.0267901166931463;83431!GO:0048667;neuron morphogenesis during differentiation;0.0267901166931463;83431!GO:0048812;neurite morphogenesis;0.0267901166931463;83431!GO:0007017;microtubule-based process;0.0279936307420963;83431!GO:0000904;cellular morphogenesis during differentiation;0.0282789936223216;83431!GO:0005874;microtubule;0.0282789936223216;83431!GO:0031175;neurite development;0.0282789936223216;83431!GO:0048666;neuron development;0.0298507020689676;83431!GO:0043009;chordate embryonic development;0.0298507020689676;83431!GO:0009792;embryonic development ending in birth or egg hatching;0.0298507020689676;83431!GO:0007417;central nervous system development;0.0299734434426064;83431!GO:0032990;cell part morphogenesis;0.0317628577143738;83431!GO:0030030;cell projection organization and biogenesis;0.0317628577143738;83431!GO:0048858;cell projection morphogenesis;0.0317628577143738;83431!GO:0016477;cell migration;0.0317628577143738;83431!GO:0030182;neuron differentiation;0.0317628577143738;83431!GO:0015630;microtubule cytoskeleton;0.0320495261052978;83431!GO:0048699;generation of neurons;0.0339903321051276;83431!GO:0051674;localization of cell;0.0339903321051276;83431!GO:0006928;cell motility;0.0339903321051276;83431!GO:0008092;cytoskeletal protein binding;0.0340117419892956;83431!GO:0022008;neurogenesis;0.0340117419892956;83431!GO:0042995;cell projection;0.0358954692379335;83431!GO:0009790;embryonic development;0.0414178491206925;83431!GO:0007010;cytoskeleton organization and biogenesis;0.0414178491206925;83431!GO:0000902;cell morphogenesis;0.0414178491206925;83431!GO:0032989;cellular structure morphogenesis;0.0414178491206925;83431!GO:0008283;cell proliferation;0.0414178491206925;83431!GO:0044430;cytoskeletal part;0.0457850372932825;83431!GO:0046907;intracellular 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|gostat_on_MCL_coexpression=GO:0008090;retrograde axon cargo transport;0.00704385189127424;83431!GO:0047496;vesicle transport along microtubule;0.00704385189127424;83431!GO:0001833;inner cell mass cell proliferation;0.00704385189127424;83431!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.00704385189127424;83431!GO:0060053;neurofilament cytoskeleton;0.00704385189127424;83431!GO:0021955;central nervous system neuron axonogenesis;0.00704385189127424;83431!GO:0008088;axon cargo transport;0.00704385189127424;83431!GO:0001832;blastocyst growth;0.00801238152632444;83431!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.00931353750068482;83431!GO:0045103;intermediate filament-based process;0.00941314752743011;83431!GO:0021954;central nervous system neuron development;0.00941314752743011;83431!GO:0021953;central nervous system neuron differentiation;0.00986139264778393;83431!GO:0001824;blastocyst development;0.0117578143108193;83431!GO:0005813;centrosome;0.0142730683060031;83431!GO:0008017;microtubule binding;0.0142730683060031;83431!GO:0048589;developmental growth;0.0142730683060031;83431!GO:0005815;microtubule organizing center;0.0142730683060031;83431!GO:0015631;tubulin binding;0.0142730683060031;83431!GO:0001764;neuron migration;0.0142730683060031;83431!GO:0030424;axon;0.0150268840347184;83431!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0150268840347184;83431!GO:0007018;microtubule-based movement;0.0186021724946833;83431!GO:0030705;cytoskeleton-dependent intracellular transport;0.0209554593765408;83431!GO:0005875;microtubule associated complex;0.0209554593765408;83431!GO:0043005;neuron projection;0.0220968242663307;83431!GO:0001701;in utero embryonic development;0.0220968242663307;83431!GO:0045111;intermediate filament cytoskeleton;0.0220968242663307;83431!GO:0007409;axonogenesis;0.0267901166931463;83431!GO:0048667;neuron morphogenesis during differentiation;0.0267901166931463;83431!GO:0048812;neurite morphogenesis;0.0267901166931463;83431!GO:0007017;microtubule-based process;0.0279936307420963;83431!GO:0000904;cellular morphogenesis during differentiation;0.0282789936223216;83431!GO:0005874;microtubule;0.0282789936223216;83431!GO:0031175;neurite development;0.0282789936223216;83431!GO:0048666;neuron development;0.0298507020689676;83431!GO:0043009;chordate embryonic development;0.0298507020689676;83431!GO:0009792;embryonic development ending in birth or egg hatching;0.0298507020689676;83431!GO:0007417;central nervous system development;0.0299734434426064;83431!GO:0032990;cell part morphogenesis;0.0317628577143738;83431!GO:0030030;cell projection organization and biogenesis;0.0317628577143738;83431!GO:0048858;cell projection morphogenesis;0.0317628577143738;83431!GO:0016477;cell migration;0.0317628577143738;83431!GO:0030182;neuron differentiation;0.0317628577143738;83431!GO:0015630;microtubule cytoskeleton;0.0320495261052978;83431!GO:0048699;generation of neurons;0.0339903321051276;83431!GO:0051674;localization of cell;0.0339903321051276;83431!GO:0006928;cell motility;0.0339903321051276;83431!GO:0008092;cytoskeletal protein binding;0.0340117419892956;83431!GO:0022008;neurogenesis;0.0340117419892956;83431!GO:0042995;cell projection;0.0358954692379335;83431!GO:0009790;embryonic development;0.0414178491206925;83431!GO:0007010;cytoskeleton organization and biogenesis;0.0414178491206925;83431!GO:0000902;cell morphogenesis;0.0414178491206925;83431!GO:0032989;cellular structure morphogenesis;0.0414178491206925;83431!GO:0008283;cell proliferation;0.0414178491206925;83431!GO:0044430;cytoskeletal part;0.0457850372932825;83431!GO:0046907;intracellular transport;0.049133956350362;83431!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000014!1.28e-08!5;UBERON:0001003!1.28e-08!5;UBERON:0002097!1.28e-08!5;UBERON:0002199!1.28e-08!5;UBERON:0007029!1.28e-08!5;UBERON:0007376!1.28e-08!5;UBERON:0002416!1.28e-08!5;UBERON:0007383!1.28e-08!5
}}

Latest revision as of 18:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:68673507..68673519,-p9@Ndel1
Mm9::chr11:68673524..68673565,-p5@Ndel1
Mm9::chr18:61696224..61696237,-p4@Arhgef37


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

GO IDGO nameFDR corrected p-value
GO:0008090retrograde axon cargo transport0.00704385189127424
GO:0047496vesicle transport along microtubule0.00704385189127424
GO:0001833inner cell mass cell proliferation0.00704385189127424
GO:0060052neurofilament cytoskeleton organization and biogenesis0.00704385189127424
GO:0060053neurofilament cytoskeleton0.00704385189127424
GO:0021955central nervous system neuron axonogenesis0.00704385189127424
GO:0008088axon cargo transport0.00704385189127424
GO:0001832blastocyst growth0.00801238152632444
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.00931353750068482
GO:0045103intermediate filament-based process0.00941314752743011
GO:0021954central nervous system neuron development0.00941314752743011
GO:0021953central nervous system neuron differentiation0.00986139264778393
GO:0001824blastocyst development0.0117578143108193
GO:0005813centrosome0.0142730683060031
GO:0008017microtubule binding0.0142730683060031
GO:0048589developmental growth0.0142730683060031
GO:0005815microtubule organizing center0.0142730683060031
GO:0015631tubulin binding0.0142730683060031
GO:0001764neuron migration0.0142730683060031
GO:0030424axon0.0150268840347184
GO:0000226microtubule cytoskeleton organization and biogenesis0.0150268840347184
GO:0007018microtubule-based movement0.0186021724946833
GO:0030705cytoskeleton-dependent intracellular transport0.0209554593765408
GO:0005875microtubule associated complex0.0209554593765408
GO:0043005neuron projection0.0220968242663307
GO:0001701in utero embryonic development0.0220968242663307
GO:0045111intermediate filament cytoskeleton0.0220968242663307
GO:0007409axonogenesis0.0267901166931463
GO:0048667neuron morphogenesis during differentiation0.0267901166931463
GO:0048812neurite morphogenesis0.0267901166931463
GO:0007017microtubule-based process0.0279936307420963
GO:0000904cellular morphogenesis during differentiation0.0282789936223216
GO:0005874microtubule0.0282789936223216
GO:0031175neurite development0.0282789936223216
GO:0048666neuron development0.0298507020689676
GO:0043009chordate embryonic development0.0298507020689676
GO:0009792embryonic development ending in birth or egg hatching0.0298507020689676
GO:0007417central nervous system development0.0299734434426064
GO:0032990cell part morphogenesis0.0317628577143738
GO:0030030cell projection organization and biogenesis0.0317628577143738
GO:0048858cell projection morphogenesis0.0317628577143738
GO:0016477cell migration0.0317628577143738
GO:0030182neuron differentiation0.0317628577143738
GO:0015630microtubule cytoskeleton0.0320495261052978
GO:0048699generation of neurons0.0339903321051276
GO:0051674localization of cell0.0339903321051276
GO:0006928cell motility0.0339903321051276
GO:0008092cytoskeletal protein binding0.0340117419892956
GO:0022008neurogenesis0.0340117419892956
GO:0042995cell projection0.0358954692379335
GO:0009790embryonic development0.0414178491206925
GO:0007010cytoskeleton organization and biogenesis0.0414178491206925
GO:0000902cell morphogenesis0.0414178491206925
GO:0032989cellular structure morphogenesis0.0414178491206925
GO:0008283cell proliferation0.0414178491206925
GO:0044430cytoskeletal part0.0457850372932825
GO:0046907intracellular transport0.049133956350362



Relative expression of the co-expression cluster over median <br>Analyst:




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>

Uber Anatomy
Ontology termp-valuen
zone of skin1.28e-085
skin epidermis1.28e-085
skin of body1.28e-085
integument1.28e-085
surface1.28e-085
outer epithelium1.28e-085
integumental system1.28e-085
enveloping layer of ectoderm1.28e-085


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

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.12.84671
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.11.66457
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.11.56167
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.794492
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.22.04809
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.12.15144
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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