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MCL coexpression mm9:264: Difference between revisions

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{{MCL_coexpression_mm9
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receptor protein serine/threonine kinase signaling pathway;0.0276058484853454;20742,11641!GO:0007527;adult somatic muscle development;0.0276058484853454;22288!GO:0030036;actin cytoskeleton organization and biogenesis;0.0276058484853454;20742,11641!GO:0030029;actin filament-based process;0.0276058484853454;20742,11641!GO:0007525;somatic muscle development;0.0276058484853454;22288!GO:0007184;SMAD protein nuclear translocation;0.0306698039093664;20742!GO:0004499;flavin-containing monooxygenase activity;0.0328569034321639;14261!GO:0003779;actin binding;0.0358052730957127;20742,22288!GO:0007167;enzyme linked receptor protein signaling pathway;0.0367876359540371;20742,11641!GO:0051018;protein kinase A binding;0.0367876359540371;11641!GO:0007182;common-partner SMAD protein phosphorylation;0.0376195958943488;20742!GO:0050661;NADP binding;0.0393980510213329;14261!GO:0008092;cytoskeletal protein binding;0.0393980510213329;20742,22288!GO:0016010;dystrophin-associated glycoprotein complex;0.0393980510213329;22288!GO:0031594;neuromuscular junction;0.039831442055262;22288!GO:0000060;protein import into nucleus, translocation;0.0404043651360832;20742!GO:0051016;barbed-end actin filament capping;0.0404043651360832;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0051693;actin filament capping;0.0404043651360832;20742!GO:0005624;membrane fraction;0.0404043651360832;22288,14261!GO:0007010;cytoskeleton organization and biogenesis;0.0404043651360832;20742,11641!GO:0030834;regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0030042;actin filament depolymerization;0.0404043651360832;20742!GO:0007165;signal transduction;0.0404043651360832;20742,11641,22288,224792!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0404043651360832;14261!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0406118255343949;14261!GO:0000267;cell fraction;0.0421358455079084;22288,14261!GO:0005605;basal lamina;0.0421358455079084;22288!GO:0007154;cell communication;0.0421358455079084;20742,11641,22288,224792!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0421358455079084;20742!GO:0051261;protein depolymerization;0.0421358455079084;20742!GO:0032535;regulation of cellular component size;0.0421358455079084;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0030832;regulation of actin filament length;0.0421358455079084;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0421358455079084;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0421358455079084;20742!GO:0008154;actin polymerization and/or depolymerization;0.0469985389384137;20742!GO:0007015;actin filament 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|gostat_on_MCL_coexpression=GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0276058484853454;20742,11641!GO:0007527;adult somatic muscle development;0.0276058484853454;22288!GO:0030036;actin cytoskeleton organization and biogenesis;0.0276058484853454;20742,11641!GO:0030029;actin filament-based process;0.0276058484853454;20742,11641!GO:0007525;somatic muscle development;0.0276058484853454;22288!GO:0007184;SMAD protein nuclear translocation;0.0306698039093664;20742!GO:0004499;flavin-containing monooxygenase activity;0.0328569034321639;14261!GO:0003779;actin binding;0.0358052730957127;20742,22288!GO:0007167;enzyme linked receptor protein signaling pathway;0.0367876359540371;20742,11641!GO:0051018;protein kinase A binding;0.0367876359540371;11641!GO:0007182;common-partner SMAD protein phosphorylation;0.0376195958943488;20742!GO:0050661;NADP binding;0.0393980510213329;14261!GO:0008092;cytoskeletal protein binding;0.0393980510213329;20742,22288!GO:0016010;dystrophin-associated glycoprotein complex;0.0393980510213329;22288!GO:0031594;neuromuscular junction;0.039831442055262;22288!GO:0000060;protein import into nucleus, translocation;0.0404043651360832;20742!GO:0051016;barbed-end actin filament capping;0.0404043651360832;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0051693;actin filament capping;0.0404043651360832;20742!GO:0005624;membrane fraction;0.0404043651360832;22288,14261!GO:0007010;cytoskeleton organization and biogenesis;0.0404043651360832;20742,11641!GO:0030834;regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0030042;actin filament depolymerization;0.0404043651360832;20742!GO:0007165;signal transduction;0.0404043651360832;20742,11641,22288,224792!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0404043651360832;14261!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0406118255343949;14261!GO:0000267;cell fraction;0.0421358455079084;22288,14261!GO:0005605;basal lamina;0.0421358455079084;22288!GO:0007154;cell communication;0.0421358455079084;20742,11641,22288,224792!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0421358455079084;20742!GO:0051261;protein depolymerization;0.0421358455079084;20742!GO:0032535;regulation of cellular component size;0.0421358455079084;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0030832;regulation of actin filament length;0.0421358455079084;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0421358455079084;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0421358455079084;20742!GO:0008154;actin polymerization and/or depolymerization;0.0469985389384137;20742!GO:0007015;actin filament organization;0.0469985389384137;11641!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!1.37e-09!14;UBERON:0000117!1.37e-09!14;UBERON:0000171!1.37e-09!14;UBERON:0000170!1.37e-09!14;UBERON:0005597!1.37e-09!14;UBERON:0000118!1.37e-09!14;UBERON:0009569!2.12e-09!66;UBERON:0005177!4.18e-09!79;UBERON:0004872!3.76e-08!33;UBERON:0007100!2.37e-07!18;UBERON:0000948!2.37e-07!18;UBERON:0005498!2.37e-07!18;UBERON:0004140!2.37e-07!18;UBERON:0009881!2.37e-07!18;UBERON:0004141!2.37e-07!18;UBERON:0003084!2.37e-07!18;UBERON:0007005!2.37e-07!18;UBERON:0004139!2.37e-07!18;UBERON:0004291!2.37e-07!18;UBERON:0005153!6.13e-07!17;UBERON:0005178!6.13e-07!17;UBERON:0005181!6.13e-07!17;UBERON:0002224!6.13e-07!17;UBERON:0000915!6.13e-07!17;UBERON:0008947!6.13e-07!17;UBERON:0003258!6.13e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.224432,0.00881107,0.0525978,0.0803981,0.224548,0.293623,0.134128,0.365336,0.0364261,0.0244587,0.110217,0.127377,0.0951638,0.435601,0.252098,0,0.268829,0.0835981,0.0796869,0.0500774,0.644017,0.179381,0.140634,0.424756,0.203316,0.157469,0.161038,0.0971006,0.127587,0.038458,0.0902787,0.914618,0.0819465,0.243363,0.0240863,0.0237332,0.0163998,0.125378,0.16226,0.0443679,0.218099,0.0927543,0.690762,0.479427,0.00259217,0.0754546,0.212558,0.34211,0.70463,0.130273,0.256131,0.174075,0.170383,0.462148,0.477006,0.145324,1.32901,0.120379,0.0637775,0.14413,0.330215,0.180052,0.248699,0.248044,0.15191,0.277492,0.596353,0.920398,0.326579,0.781435,0.0459805,0.383821,0.000226454,0.505848,0.00296685,0.0495257,0.0550687,0.204903,0.849865,0.367316,0.218909,0.28165,0.179134,0.801815,0.408287,6.58821e-06,1.66148,0.0944002,0.215887,1.07627,0.659258,1.06069,0.356069,0.722184,0.0120375,1.02896,0.566539,0.358304,0.212731,0.0071244,0.194195,0.345703,0.44741,0.71262,0.255799,0.0925422,0.299999,0.336675,0.165666,0.0407056,0.216311,0.448913,0.369514,0.112926,0.665677,0.67732,0.00517752,0.0821019,0.269784,0.61238,0.510527,0.233232,0.158574,0.59017,0.715313,0.319766,0.847582,0.35069,0.594996,0.239081,1.10577,0.0771462,0.568676,0.466342,0.685415,0.00669601,0.0659275,0.311081,0.640623,1.43657,1.04548,0.600569,0.497375,0.354213,0.25114,0.0929729,0.214675,1.39749,0.0668942,0.0206358,0.00177339,0.000115804,0.46348,0.0103473,0.464961,0.533955,0.518839,0.811415,0.832173,0.0658133,0.649247,0.407582,0.32011,0.213736,0.248774,0.148453,0.192381,0.794153,7.83586e-06
|tfbs_overrepresentation_jaspar=MA0003.1;9.51468e-06,MA0004.1;0.275884,MA0006.1;0.0229559,MA0007.1;0.547029,MA0009.1;0.961172,MA0014.1;6.95485e-06,MA0017.1;0.0294752,MA0019.1;0.650431,MA0024.1;0.332319,MA0025.1;0.564682,MA0027.1;1.93116,MA0028.1;0.0253985,MA0029.1;0.315482,MA0030.1;2.3515,MA0031.1;0.79685,MA0038.1;0.476304,MA0040.1;0.983355,MA0041.1;0.735309,MA0042.1;2.57949,MA0043.1;0.446565,MA0046.1;0.396073,MA0048.1;0.0268917,MA0050.1;0.326024,MA0051.1;0.948956,MA0052.1;0.997688,MA0055.1;0.0199141,MA0056.1;0,MA0057.1;0.0564077,MA0058.1;0.378396,MA0059.1;0.179276,MA0060.1;0.00889506,MA0061.1;0.332043,MA0063.1;0,MA0066.1;0.898799,MA0067.1;0.664516,MA0068.1;0.060674,MA0069.1;0.383839,MA0070.1;0.37599,MA0071.1;0.324912,MA0072.1;0.369163,MA0073.1;2.5122,MA0074.1;0.130125,MA0076.1;0.139184,MA0077.1;0.351866,MA0078.1;0.540438,MA0081.1;0.449942,MA0083.1;0.445897,MA0084.1;0.971934,MA0087.1;0.409958,MA0088.1;0.023289,MA0089.1;0,MA0090.1;0.234247,MA0091.1;0.0866349,MA0092.1;0.234618,MA0093.1;0.276659,MA0095.1;0,MA0098.1;0,MA0100.1;0.781912,MA0101.1;0.18882,MA0103.1;0.131431,MA0105.1;0.0156648,MA0106.1;0.188607,MA0107.1;0.298859,MA0108.2;0.245881,MA0109.1;0,MA0111.1;0.251142,MA0113.1;0.508933,MA0114.1;0.0128073,MA0115.1;0.448923,MA0116.1;0.022909,MA0117.1;0.42191,MA0119.1;0.0507723,MA0122.1;0.438479,MA0124.1;0.616327,MA0125.1;0.55037,MA0130.1;0,MA0131.1;0.226654,MA0132.1;0,MA0133.1;0,MA0135.1;0.477472,MA0136.1;0.859001,MA0139.1;0.0305298,MA0140.1;0.390942,MA0141.1;0.624652,MA0142.1;1.41035,MA0143.1;1.6191,MA0144.1;0.333849,MA0145.1;0.0663158,MA0146.1;0.00208601,MA0147.1;0.0714602,MA0148.1;0.617074,MA0149.1;0.0525422,MA0062.2;0.0171722,MA0035.2;0.397603,MA0039.2;3.42906e-05,MA0138.2;0.630162,MA0002.2;0.0938694,MA0137.2;0.147294,MA0104.2;0.0382807,MA0047.2;0.924448,MA0112.2;0.00980622,MA0065.2;0.0668461,MA0150.1;0.929689,MA0151.1;0,MA0152.1;0.475315,MA0153.1;0.491737,MA0154.1;0.0666513,MA0155.1;0.0142364,MA0156.1;0.138367,MA0157.1;0.718286,MA0158.1;0,MA0159.1;0.0785092,MA0160.1;0.623941,MA0161.1;0,MA0162.1;3.21658e-06,MA0163.1;0.000800664,MA0164.1;0.859898,MA0080.2;0.300456,MA0018.2;0.147322,MA0099.2;0.216863,MA0079.2;3.03902e-05,MA0102.2;1.0223,MA0258.1;0.0532628,MA0259.1;0.064381,MA0442.1;0
}}

Latest revision as of 14:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115726435..115726454,+p@chr10:115726435..115726454
+
Mm9::chr10:115783936..115783945,+p@chr10:115783936..115783945
+
Mm9::chr10:115809917..115809921,+p@chr10:115809917..115809921
+
Mm9::chr10:12103662..12103666,-p@chr10:12103662..12103666
-
Mm9::chr11:30000318..30000322,-p@chr11:30000318..30000322
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Mm9::chr11:30148502..30148509,-p@chr11:30148502..30148509
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Mm9::chr11:30153416..30153420,-p@chr11:30153416..30153420
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Mm9::chr13:100017650..100017662,+p@chr13:100017650..100017662
+
Mm9::chr13:115846729..115846733,-p@chr13:115846729..115846733
-
Mm9::chr16:85542827..85542835,-p@chr16:85542827..85542835
-
Mm9::chr16:95581011..95581024,-p@chr16:95581011..95581024
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Mm9::chr17:13016269..13016283,+p@chr17:13016269..13016283
+
Mm9::chr17:43592386..43592398,+p@chr17:43592386..43592398
+
Mm9::chr17:43592580..43592605,+p@chr17:43592580..43592605
+
Mm9::chr17:47898459..47898487,+p@chr17:47898459..47898487
+
Mm9::chr17:67475291..67475294,-p@chr17:67475291..67475294
-
Mm9::chr17:75919962..75919967,+p@chr17:75919962..75919967
+
Mm9::chr19:21867742..21867746,+p@chr19:21867742..21867746
+
Mm9::chr1:11175335..11175339,+p@chr1:11175335..11175339
+
Mm9::chr1:152644349..152644352,-p@chr1:152644349..152644352
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Mm9::chr1:164764434..164764438,-p13@Fmo1
Mm9::chr1:59931940..59931964,+p@chr1:59931940..59931964
+
Mm9::chr2:84247734..84247745,-p@chr2:84247734..84247745
-
Mm9::chr4:3706358..3706404,+p@chr4:3706358..3706404
+
Mm9::chr4:57906800..57906812,+p@chr4:57906800..57906812
+
Mm9::chr4:94487460..94487476,+p@chr4:94487460..94487476
+
Mm9::chr5:65546218..65546229,+p@chr5:65546218..65546229
+
Mm9::chr5:65546334..65546342,+p@chr5:65546334..65546342
+
Mm9::chr6:97469086..97469090,-p@chr6:97469086..97469090
-
Mm9::chr7:108156311..108156321,-p@chr7:108156311..108156321
-
Mm9::chr8:37649789..37649792,-p@chr8:37649789..37649792
-


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:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0276058484853454
GO:0007527adult somatic muscle development0.0276058484853454
GO:0030036actin cytoskeleton organization and biogenesis0.0276058484853454
GO:0030029actin filament-based process0.0276058484853454
GO:0007525somatic muscle development0.0276058484853454
GO:0007184SMAD protein nuclear translocation0.0306698039093664
GO:0004499flavin-containing monooxygenase activity0.0328569034321639
GO:0003779actin binding0.0358052730957127
GO:0007167enzyme linked receptor protein signaling pathway0.0367876359540371
GO:0051018protein kinase A binding0.0367876359540371
GO:0007182common-partner SMAD protein phosphorylation0.0376195958943488
GO:0050661NADP binding0.0393980510213329
GO:0008092cytoskeletal protein binding0.0393980510213329
GO:0016010dystrophin-associated glycoprotein complex0.0393980510213329
GO:0031594neuromuscular junction0.039831442055262
GO:0000060protein import into nucleus, translocation0.0404043651360832
GO:0051016barbed-end actin filament capping0.0404043651360832
GO:0030835negative regulation of actin filament depolymerization0.0404043651360832
GO:0051693actin filament capping0.0404043651360832
GO:0005624membrane fraction0.0404043651360832
GO:0007010cytoskeleton organization and biogenesis0.0404043651360832
GO:0030834regulation of actin filament depolymerization0.0404043651360832
GO:0030042actin filament depolymerization0.0404043651360832
GO:0007165signal transduction0.0404043651360832
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0404043651360832
GO:0031227intrinsic to endoplasmic reticulum membrane0.0406118255343949
GO:0000267cell fraction0.0421358455079084
GO:0005605basal lamina0.0421358455079084
GO:0007154cell communication0.0421358455079084
GO:0008064regulation of actin polymerization and/or depolymerization0.0421358455079084
GO:0051261protein depolymerization0.0421358455079084
GO:0032535regulation of cellular component size0.0421358455079084
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0421358455079084
GO:0030832regulation of actin filament length0.0421358455079084
GO:0051129negative regulation of cellular component organization and biogenesis0.0421358455079084
GO:0051493regulation of cytoskeleton organization and biogenesis0.0421358455079084
GO:0033043regulation of organelle organization and biogenesis0.0421358455079084
GO:0008154actin polymerization and/or depolymerization0.0469985389384137
GO:0007015actin filament organization0.0469985389384137



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>


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)
MA0003.19.51468e-06
MA0004.10.275884
MA0006.10.0229559
MA0007.10.547029
MA0009.10.961172
MA0014.16.95485e-06
MA0017.10.0294752
MA0019.10.650431
MA0024.10.332319
MA0025.10.564682
MA0027.11.93116
MA0028.10.0253985
MA0029.10.315482
MA0030.12.3515
MA0031.10.79685
MA0038.10.476304
MA0040.10.983355
MA0041.10.735309
MA0042.12.57949
MA0043.10.446565
MA0046.10.396073
MA0048.10.0268917
MA0050.10.326024
MA0051.10.948956
MA0052.10.997688
MA0055.10.0199141
MA0056.10
MA0057.10.0564077
MA0058.10.378396
MA0059.10.179276
MA0060.10.00889506
MA0061.10.332043
MA0063.10
MA0066.10.898799
MA0067.10.664516
MA0068.10.060674
MA0069.10.383839
MA0070.10.37599
MA0071.10.324912
MA0072.10.369163
MA0073.12.5122
MA0074.10.130125
MA0076.10.139184
MA0077.10.351866
MA0078.10.540438
MA0081.10.449942
MA0083.10.445897
MA0084.10.971934
MA0087.10.409958
MA0088.10.023289
MA0089.10
MA0090.10.234247
MA0091.10.0866349
MA0092.10.234618
MA0093.10.276659
MA0095.10
MA0098.10
MA0100.10.781912
MA0101.10.18882
MA0103.10.131431
MA0105.10.0156648
MA0106.10.188607
MA0107.10.298859
MA0108.20.245881
MA0109.10
MA0111.10.251142
MA0113.10.508933
MA0114.10.0128073
MA0115.10.448923
MA0116.10.022909
MA0117.10.42191
MA0119.10.0507723
MA0122.10.438479
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.10.226654
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.859001
MA0139.10.0305298
MA0140.10.390942
MA0141.10.624652
MA0142.11.41035
MA0143.11.6191
MA0144.10.333849
MA0145.10.0663158
MA0146.10.00208601
MA0147.10.0714602
MA0148.10.617074
MA0149.10.0525422
MA0062.20.0171722
MA0035.20.397603
MA0039.23.42906e-05
MA0138.20.630162
MA0002.20.0938694
MA0137.20.147294
MA0104.20.0382807
MA0047.20.924448
MA0112.20.00980622
MA0065.20.0668461
MA0150.10.929689
MA0151.10
MA0152.10.475315
MA0153.10.491737
MA0154.10.0666513
MA0155.10.0142364
MA0156.10.138367
MA0157.10.718286
MA0158.10
MA0159.10.0785092
MA0160.10.623941
MA0161.10
MA0162.13.21658e-06
MA0163.10.000800664
MA0164.10.859898
MA0080.20.300456
MA0018.20.147322
MA0099.20.216863
MA0079.23.03902e-05
MA0102.21.0223
MA0258.10.0532628
MA0259.10.064381
MA0442.10
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