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MCL coexpression mm9:2657: Difference between revisions

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{{MCL_coexpression_mm9
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protein nuclear translocation;0.0214017713190662;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0214017713190662;20742!GO:0000060;protein import into nucleus, translocation;0.0214017713190662;20742!GO:0051016;barbed-end actin filament capping;0.0214017713190662;20742!GO:0051693;actin filament capping;0.0214017713190662;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0214017713190662;20742!GO:0030834;regulation of actin filament depolymerization;0.0214017713190662;20742!GO:0030042;actin filament depolymerization;0.0214017713190662;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0214017713190662;20742!GO:0051261;protein depolymerization;0.0214017713190662;20742!GO:0032535;regulation of cellular component size;0.0214017713190662;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0214017713190662;20742!GO:0030832;regulation of actin filament length;0.0214017713190662;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0214017713190662;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0214017713190662;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0214017713190662;20742!GO:0008154;actin polymerization and/or depolymerization;0.0236935644813801;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0257296093639118;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0273194767334824;20742!GO:0006606;protein import into nucleus;0.0273194767334824;20742!GO:0051170;nuclear import;0.0273194767334824;20742!GO:0017038;protein import;0.0292745813355702;20742!GO:0051248;negative regulation of protein metabolic process;0.0297486185327594;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0331108588792257;20742!GO:0006913;nucleocytoplasmic transport;0.0359664230322438;20742!GO:0051169;nuclear transport;0.0359664230322438;20742!GO:0005516;calmodulin 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|gostat_on_MCL_coexpression=GO:0007184;SMAD protein nuclear translocation;0.0214017713190662;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0214017713190662;20742!GO:0000060;protein import into nucleus, translocation;0.0214017713190662;20742!GO:0051016;barbed-end actin filament capping;0.0214017713190662;20742!GO:0051693;actin filament capping;0.0214017713190662;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0214017713190662;20742!GO:0030834;regulation of actin filament depolymerization;0.0214017713190662;20742!GO:0030042;actin filament depolymerization;0.0214017713190662;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0214017713190662;20742!GO:0051261;protein depolymerization;0.0214017713190662;20742!GO:0032535;regulation of cellular component size;0.0214017713190662;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0214017713190662;20742!GO:0030832;regulation of actin filament length;0.0214017713190662;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0214017713190662;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0214017713190662;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0214017713190662;20742!GO:0008154;actin polymerization and/or depolymerization;0.0236935644813801;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0257296093639118;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0273194767334824;20742!GO:0006606;protein import into nucleus;0.0273194767334824;20742!GO:0051170;nuclear import;0.0273194767334824;20742!GO:0017038;protein import;0.0292745813355702;20742!GO:0051248;negative regulation of protein metabolic process;0.0297486185327594;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0331108588792257;20742!GO:0006913;nucleocytoplasmic transport;0.0359664230322438;20742!GO:0051169;nuclear transport;0.0359664230322438;20742!GO:0005516;calmodulin binding;0.0398327827502721;20742!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!1.11e-17!47;UBERON:0000160!3.01e-16!31;UBERON:0004119!2.89e-15!118;UBERON:0000925!2.89e-15!118;UBERON:0006595!2.89e-15!118;UBERON:0001007!3.17e-14!116;UBERON:0001555!3.17e-14!116;UBERON:0007026!3.17e-14!116;UBERON:0004921!3.16e-13!114;UBERON:0005177!5.04e-09!79;UBERON:0000344!1.14e-08!15;UBERON:0004923!1.60e-08!24;UBERON:0002100!6.34e-08!90;UBERON:0001242!1.59e-07!13;UBERON:0000060!1.59e-07!13;UBERON:0001262!1.59e-07!13;UBERON:0004786!1.59e-07!13;UBERON:0001008!6.70e-07!19;UBERON:0006554!8.36e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.138,0.876292,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.444545,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.724277,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,2.80351,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,1.50904,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 18:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:30097829..30097850,-p7@Spnb2
Mm9::chr11:30097856..30097896,-p6@Spnb2
Mm9::chr17:35051377..35051391,+p2@Slc44a4


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:0007184SMAD protein nuclear translocation0.0214017713190662
GO:0007182common-partner SMAD protein phosphorylation0.0214017713190662
GO:0000060protein import into nucleus, translocation0.0214017713190662
GO:0051016barbed-end actin filament capping0.0214017713190662
GO:0051693actin filament capping0.0214017713190662
GO:0030835negative regulation of actin filament depolymerization0.0214017713190662
GO:0030834regulation of actin filament depolymerization0.0214017713190662
GO:0030042actin filament depolymerization0.0214017713190662
GO:0008064regulation of actin polymerization and/or depolymerization0.0214017713190662
GO:0051261protein depolymerization0.0214017713190662
GO:0032535regulation of cellular component size0.0214017713190662
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0214017713190662
GO:0030832regulation of actin filament length0.0214017713190662
GO:0051493regulation of cytoskeleton organization and biogenesis0.0214017713190662
GO:0033043regulation of organelle organization and biogenesis0.0214017713190662
GO:0051129negative regulation of cellular component organization and biogenesis0.0214017713190662
GO:0008154actin polymerization and/or depolymerization0.0236935644813801
GO:0007179transforming growth factor beta receptor signaling pathway0.0257296093639118
GO:0051128regulation of cellular component organization and biogenesis0.0273194767334824
GO:0006606protein import into nucleus0.0273194767334824
GO:0051170nuclear import0.0273194767334824
GO:0017038protein import0.0292745813355702
GO:0051248negative regulation of protein metabolic process0.0297486185327594
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0331108588792257
GO:0006913nucleocytoplasmic transport0.0359664230322438
GO:0051169nuclear transport0.0359664230322438
GO:0005516calmodulin binding0.0398327827502721



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
gastrointestinal system1.11e-1747
intestine3.01e-1631
endoderm-derived structure2.89e-15118
endoderm2.89e-15118
presumptive endoderm2.89e-15118
digestive system3.17e-14116
digestive tract3.17e-14116
primitive gut3.17e-14116
subdivision of digestive tract3.16e-13114
trunk region element5.04e-0979
mucosa1.14e-0815
organ component layer1.60e-0824
trunk6.34e-0890
intestinal mucosa1.59e-0713
anatomical wall1.59e-0713
wall of intestine1.59e-0713
gastrointestinal system mucosa1.59e-0713
renal system6.70e-0719
urinary system structure8.36e-0718


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
MA0009.11.27673
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
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.121346
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.11.54626
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
MA0144.12.29766
MA0145.11.44606
MA0146.10.900029
MA0147.10.556853
MA0148.10.820161
MA0149.12.8784
MA0062.21.06145
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.21.17677
MA0137.21.60348
MA0104.20.48458
MA0047.20.962424
MA0112.20.794478
MA0065.20.79573
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.157796
MA0164.10.933981
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.0831329
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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