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MCL coexpression mm9:2748: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0016573;histone acetylation;0.0121075987508903;22658!GO:0031519;PcG protein complex;0.0121075987508903;22658!GO:0006473;protein amino acid acetylation;0.0121075987508903;22658!GO:0001739;sex chromatin;0.0121075987508903;22658!GO:0000803;sex chromosome;0.0121075987508903;22658!GO:0043543;protein amino acid acylation;0.0147464343760843;22658!GO:0005720;nuclear heterochromatin;0.0147464343760843;22658!GO:0000790;nuclear chromatin;0.0147464343760843;22658!GO:0016570;histone modification;0.0147464343760843;22658!GO:0000792;heterochromatin;0.0147464343760843;22658!GO:0016569;covalent chromatin modification;0.0147464343760843;22658!GO:0016604;nuclear body;0.0147464343760843;22658!GO:0044454;nuclear chromosome part;0.0240002697133032;22658!GO:0000228;nuclear chromosome;0.0259448544661934;22658!GO:0009952;anterior/posterior pattern formation;0.0288137566427437;22658!GO:0003682;chromatin binding;0.0288137566427437;22658!GO:0003002;regionalization;0.0402673533117844;22658!GO:0016568;chromatin modification;0.0426870468781387;22658!GO:0000785;chromatin;0.047302966779794;22658!}}
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acetylation;0.0121075987508903;22658!GO:0031519;PcG protein complex;0.0121075987508903;22658!GO:0006473;protein amino acid acetylation;0.0121075987508903;22658!GO:0001739;sex chromatin;0.0121075987508903;22658!GO:0000803;sex chromosome;0.0121075987508903;22658!GO:0043543;protein amino acid acylation;0.0147464343760843;22658!GO:0005720;nuclear heterochromatin;0.0147464343760843;22658!GO:0000790;nuclear chromatin;0.0147464343760843;22658!GO:0016570;histone modification;0.0147464343760843;22658!GO:0000792;heterochromatin;0.0147464343760843;22658!GO:0016569;covalent chromatin modification;0.0147464343760843;22658!GO:0016604;nuclear body;0.0147464343760843;22658!GO:0044454;nuclear chromosome part;0.0240002697133032;22658!GO:0000228;nuclear chromosome;0.0259448544661934;22658!GO:0009952;anterior/posterior pattern formation;0.0288137566427437;22658!GO:0003682;chromatin binding;0.0288137566427437;22658!GO:0003002;regionalization;0.0402673533117844;22658!GO:0016568;chromatin modification;0.0426870468781387;22658!GO:0000785;chromatin;0.047302966779794;22658!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004535!9.96e-13!23;UBERON:0001009!9.96e-13!23;UBERON:0007100!9.18e-11!18;UBERON:0000948!9.18e-11!18;UBERON:0005498!9.18e-11!18;UBERON:0004140!9.18e-11!18;UBERON:0009881!9.18e-11!18;UBERON:0004141!9.18e-11!18;UBERON:0003084!9.18e-11!18;UBERON:0007005!9.18e-11!18;UBERON:0004139!9.18e-11!18;UBERON:0004291!9.18e-11!18;UBERON:0004872!2.56e-09!33;UBERON:0002048!2.91e-08!14;UBERON:0000117!2.91e-08!14;UBERON:0000171!2.91e-08!14;UBERON:0000170!2.91e-08!14;UBERON:0005597!2.91e-08!14;UBERON:0000118!2.91e-08!14;UBERON:0000468!1.68e-07!333;UBERON:0000464!3.37e-07!57;UBERON:0005153!3.95e-07!17;UBERON:0005157!5.00e-07!20;UBERON:0005178!8.06e-07!17;UBERON:0005181!8.06e-07!17;UBERON:0002224!8.06e-07!17;UBERON:0000915!8.06e-07!17;UBERON:0008947!8.06e-07!17;UBERON:0003258!8.06e-07!17|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,1.23467,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,3.02035,1.44925,2.81128,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,2.30787,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,1.32874,1.39822,1.28513,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338|tfbs_overrepresentation_jaspar=MA0003.1;2.4568,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;1.93445,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;1.60767,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;4.54623,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;1.62747,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.0430758,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;1.70277,MA0103.1;0.647985,MA0105.1;4.85283,MA0106.1;1.01755,MA0107.1;2.61846,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;2.77996,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;3.25387,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;1.21648,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.79573,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.925147,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;2.19629,MA0163.1;4.46088,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;4.99702,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0}}

Latest revision as of 19:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:97561641..97561663,-p2@Pcgf2
Mm9::chr4:123089124..123089175,-p1@D830031N03Rik
Mm9::chr4:123089245..123089260,-p2@D830031N03Rik


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:0016573histone acetylation0.0121075987508903
GO:0031519PcG protein complex0.0121075987508903
GO:0006473protein amino acid acetylation0.0121075987508903
GO:0001739sex chromatin0.0121075987508903
GO:0000803sex chromosome0.0121075987508903
GO:0043543protein amino acid acylation0.0147464343760843
GO:0005720nuclear heterochromatin0.0147464343760843
GO:0000790nuclear chromatin0.0147464343760843
GO:0016570histone modification0.0147464343760843
GO:0000792heterochromatin0.0147464343760843
GO:0016569covalent chromatin modification0.0147464343760843
GO:0016604nuclear body0.0147464343760843
GO:0044454nuclear chromosome part0.0240002697133032
GO:0000228nuclear chromosome0.0259448544661934
GO:0009952anterior/posterior pattern formation0.0288137566427437
GO:0003682chromatin binding0.0288137566427437
GO:0003002regionalization0.0402673533117844
GO:0016568chromatin modification0.0426870468781387
GO:0000785chromatin0.047302966779794



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
cardiovascular system9.96e-1323
circulatory system9.96e-1323
primary circulatory organ9.18e-1118
heart9.18e-1118
primitive heart tube9.18e-1118
primary heart field9.18e-1118
anterior lateral plate mesoderm9.18e-1118
heart tube9.18e-1118
heart primordium9.18e-1118
cardiac mesoderm9.18e-1118
cardiogenic plate9.18e-1118
heart rudiment9.18e-1118
splanchnic layer of lateral plate mesoderm2.56e-0933
lung2.91e-0814
respiratory tube2.91e-0814
respiration organ2.91e-0814
pair of lungs2.91e-0814
lung primordium2.91e-0814
lung bud2.91e-0814
multi-cellular organism1.68e-07333
anatomical space3.37e-0757
epithelial bud3.95e-0717
epithelial fold5.00e-0720
thoracic cavity element8.06e-0717
thoracic segment organ8.06e-0717
thoracic cavity8.06e-0717
thoracic segment of trunk8.06e-0717
respiratory primordium8.06e-0717
endoderm of foregut8.06e-0717


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)
MA0003.12.4568
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.93445
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
MA0057.11.60767
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.14.54623
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.11.62747
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.0430758
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
MA0101.11.70277
MA0103.10.647985
MA0105.14.85283
MA0106.11.01755
MA0107.12.61846
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
MA0145.10.292366
MA0146.12.77996
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.23.25387
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.29236
MA0065.20.79573
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.12.19629
MA0163.14.46088
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.24.99702
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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