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MCL coexpression mm9:640: Difference between revisions

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{{MCL_coexpression_mm9
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program;0.00530556953661704;107817,26401!GO:0051213;dioxygenase activity;0.00530556953661704;108829,107817!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.00530556953661704;108829,107817!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.00530556953661704;108829,107817!GO:0043010;camera-type eye development;0.00664349386223486;107817,26401!GO:0043654;recognition of apoptotic cell;0.00786563461192289;107817!GO:0008545;JUN kinase kinase activity;0.00786563461192289;26401!GO:0001654;eye development;0.00798859897006268;107817,26401!GO:0030838;positive regulation of actin filament polymerization;0.0183491254813308;26401!GO:0007423;sensory organ development;0.0200150343694242;107817,26401!GO:0043277;apoptotic cell clearance;0.0200150343694242;107817!GO:0004115;3',5'-cyclic-AMP phosphodiesterase activity;0.0229313805203644;18578!GO:0004708;MAP kinase kinase activity;0.0253981304505282;26401!GO:0004712;protein serine/threonine/tyrosine kinase activity;0.028809073084668;26401!GO:0042116;macrophage activation;0.028809073084668;107817!GO:0060041;retina development in camera-type eye;0.028809073084668;107817!GO:0048821;erythrocyte development;0.028809073084668;107817!GO:0030833;regulation of actin filament polymerization;0.028809073084668;26401!GO:0007257;activation of JNK activity;0.028809073084668;26401!GO:0043507;positive regulation of JNK activity;0.028809073084668;26401!GO:0006910;phagocytosis, recognition;0.028809073084668;107817!GO:0043506;regulation of JNK activity;0.0374829797204489;26401!GO:0004709;MAP kinase kinase kinase activity;0.0389321176228364;26401!GO:0030041;actin filament polymerization;0.0389321176228364;26401!GO:0008637;apoptotic mitochondrial changes;0.0417627181151422;26401!GO:0004114;3',5'-cyclic-nucleotide phosphodiesterase activity;0.049417168428541;18578!GO:0033077;T cell differentiation in the thymus;0.049417168428541;107817!GO:0004112;cyclic-nucleotide phosphodiesterase activity;0.049417168428541;18578!GO:0002274;myeloid leukocyte activation;0.049417168428541;107817!GO:0008064;regulation of actin polymerization and/or depolymerization;0.049417168428541;26401!GO:0008270;zinc ion binding;0.049417168428541;108829,17354,26401!GO:0032535;regulation of cellular component size;0.049417168428541;26401!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.049417168428541;26401!GO:0030832;regulation of actin filament length;0.049417168428541;26401!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.049417168428541;26401!GO:0033043;regulation of organelle organization and biogenesis;0.049417168428541;26401!GO:0000187;activation of MAPK activity;0.049417168428541;26401!GO:0030218;erythrocyte 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|gostat_on_MCL_coexpression=GO:0008632;apoptotic program;0.00530556953661704;107817,26401!GO:0051213;dioxygenase activity;0.00530556953661704;108829,107817!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.00530556953661704;108829,107817!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.00530556953661704;108829,107817!GO:0043010;camera-type eye development;0.00664349386223486;107817,26401!GO:0043654;recognition of apoptotic cell;0.00786563461192289;107817!GO:0008545;JUN kinase kinase activity;0.00786563461192289;26401!GO:0001654;eye development;0.00798859897006268;107817,26401!GO:0030838;positive regulation of actin filament polymerization;0.0183491254813308;26401!GO:0007423;sensory organ development;0.0200150343694242;107817,26401!GO:0043277;apoptotic cell clearance;0.0200150343694242;107817!GO:0004115;3',5'-cyclic-AMP phosphodiesterase activity;0.0229313805203644;18578!GO:0004708;MAP kinase kinase activity;0.0253981304505282;26401!GO:0004712;protein serine/threonine/tyrosine kinase activity;0.028809073084668;26401!GO:0042116;macrophage activation;0.028809073084668;107817!GO:0060041;retina development in camera-type eye;0.028809073084668;107817!GO:0048821;erythrocyte development;0.028809073084668;107817!GO:0030833;regulation of actin filament polymerization;0.028809073084668;26401!GO:0007257;activation of JNK activity;0.028809073084668;26401!GO:0043507;positive regulation of JNK activity;0.028809073084668;26401!GO:0006910;phagocytosis, recognition;0.028809073084668;107817!GO:0043506;regulation of JNK activity;0.0374829797204489;26401!GO:0004709;MAP kinase kinase kinase activity;0.0389321176228364;26401!GO:0030041;actin filament polymerization;0.0389321176228364;26401!GO:0008637;apoptotic mitochondrial changes;0.0417627181151422;26401!GO:0004114;3',5'-cyclic-nucleotide phosphodiesterase activity;0.049417168428541;18578!GO:0033077;T cell differentiation in the thymus;0.049417168428541;107817!GO:0004112;cyclic-nucleotide phosphodiesterase activity;0.049417168428541;18578!GO:0002274;myeloid leukocyte activation;0.049417168428541;107817!GO:0008064;regulation of actin polymerization and/or depolymerization;0.049417168428541;26401!GO:0008270;zinc ion binding;0.049417168428541;108829,17354,26401!GO:0032535;regulation of cellular component size;0.049417168428541;26401!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.049417168428541;26401!GO:0030832;regulation of actin filament length;0.049417168428541;26401!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.049417168428541;26401!GO:0033043;regulation of organelle organization and biogenesis;0.049417168428541;26401!GO:0000187;activation of MAPK activity;0.049417168428541;26401!GO:0030218;erythrocyte differentiation;0.049417168428541;107817!GO:0006915;apoptosis;0.049417168428541;107817,26401!GO:0006909;phagocytosis;0.049417168428541;107817!GO:0012501;programmed cell death;0.049417168428541;107817,26401!GO:0051258;protein polymerization;0.049417168428541;26401!GO:0008154;actin polymerization and/or depolymerization;0.049417168428541;26401!GO:0043406;positive regulation of MAP kinase activity;0.049417168428541;26401!GO:0008219;cell death;0.049417168428541;107817,26401!GO:0016265;death;0.049417168428541;107817,26401!GO:0007254;JNK cascade;0.049417168428541;26401!GO:0008037;cell recognition;0.049417168428541;107817!GO:0007179;transforming growth factor beta receptor signaling pathway;0.049417168428541;26401!GO:0031098;stress-activated protein kinase signaling pathway;0.049417168428541;26401!GO:0004702;receptor signaling protein serine/threonine kinase activity;0.049417168428541;26401!
}}

Latest revision as of 15:38, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:66648428..66648445,+p8@Jmjd1c
Mm9::chr10:66648451..66648471,+p3@Jmjd1c
Mm9::chr10:66648478..66648516,+p2@Jmjd1c
Mm9::chr10:66648821..66648848,+p9@Jmjd1c
Mm9::chr11:116704477..116704546,-p2@Jmjd6
Mm9::chr13:112598892..112598909,-p2@Map3k1
Mm9::chr15:100563143..100563171,-p1@uc007xsd.1
Mm9::chr2:17985518..17985540,+p6@Mllt10
Mm9::chr4:102243124..102243149,+p3@Pde4b
Mm9::chr5:77017688..77017767,+p1@Cep135
Mm9::chr9:72379740..72379757,+p7@Rfx7


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:0008632apoptotic program0.00530556953661704
GO:0051213dioxygenase activity0.00530556953661704
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.00530556953661704
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.00530556953661704
GO:0043010camera-type eye development0.00664349386223486
GO:0043654recognition of apoptotic cell0.00786563461192289
GO:0008545JUN kinase kinase activity0.00786563461192289
GO:0001654eye development0.00798859897006268
GO:0030838positive regulation of actin filament polymerization0.0183491254813308
GO:0007423sensory organ development0.0200150343694242
GO:0043277apoptotic cell clearance0.0200150343694242
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0229313805203644
GO:0004708MAP kinase kinase activity0.0253981304505282
GO:0004712protein serine/threonine/tyrosine kinase activity0.028809073084668
GO:0042116macrophage activation0.028809073084668
GO:0060041retina development in camera-type eye0.028809073084668
GO:0048821erythrocyte development0.028809073084668
GO:0030833regulation of actin filament polymerization0.028809073084668
GO:0007257activation of JNK activity0.028809073084668
GO:0043507positive regulation of JNK activity0.028809073084668
GO:0006910phagocytosis, recognition0.028809073084668
GO:0043506regulation of JNK activity0.0374829797204489
GO:0004709MAP kinase kinase kinase activity0.0389321176228364
GO:0030041actin filament polymerization0.0389321176228364
GO:0008637apoptotic mitochondrial changes0.0417627181151422
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.049417168428541
GO:0033077T cell differentiation in the thymus0.049417168428541
GO:0004112cyclic-nucleotide phosphodiesterase activity0.049417168428541
GO:0002274myeloid leukocyte activation0.049417168428541
GO:0008064regulation of actin polymerization and/or depolymerization0.049417168428541
GO:0008270zinc ion binding0.049417168428541
GO:0032535regulation of cellular component size0.049417168428541
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.049417168428541
GO:0030832regulation of actin filament length0.049417168428541
GO:0051493regulation of cytoskeleton organization and biogenesis0.049417168428541
GO:0033043regulation of organelle organization and biogenesis0.049417168428541
GO:0000187activation of MAPK activity0.049417168428541
GO:0030218erythrocyte differentiation0.049417168428541
GO:0006915apoptosis0.049417168428541
GO:0006909phagocytosis0.049417168428541
GO:0012501programmed cell death0.049417168428541
GO:0051258protein polymerization0.049417168428541
GO:0008154actin polymerization and/or depolymerization0.049417168428541
GO:0043406positive regulation of MAP kinase activity0.049417168428541
GO:0008219cell death0.049417168428541
GO:0016265death0.049417168428541
GO:0007254JNK cascade0.049417168428541
GO:0008037cell recognition0.049417168428541
GO:0007179transforming growth factor beta receptor signaling pathway0.049417168428541
GO:0031098stress-activated protein kinase signaling pathway0.049417168428541
GO:0004702receptor signaling protein serine/threonine kinase activity0.049417168428541



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>cell_data<br>uberon_data<br><br>


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)
MA0003.10.156602
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.44164
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.567414
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.440822
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.479469
MA0056.10
MA0057.10.048013
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.451296
MA0063.10
MA0066.11.1475
MA0067.11.08124
MA0068.10.418079
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.229055
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.0293443
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.11.85374
MA0101.10.265031
MA0103.10.619698
MA0105.10.556739
MA0106.10.509454
MA0107.10.607721
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.338099
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.452699
MA0145.10.57264
MA0146.10.0276106
MA0147.10.157258
MA0148.10.912216
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.00487869
MA0138.20.555696
MA0002.20.343346
MA0137.20.652494
MA0104.20.11535
MA0047.20.46201
MA0112.20.0329566
MA0065.20.033123
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.434137
MA0155.10.354827
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.388731
MA0163.10.198448
MA0164.10.437937
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.0743239
MA0102.21.45844
MA0258.10.135621
MA0259.10.14914
MA0442.10
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