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MCL coexpression mm9:1040: Difference between revisions

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{{MCL_coexpression_mm9
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primary transcript binding;0.023442419603706;19285!GO:0003716;RNA polymerase I transcription termination factor activity;0.023442419603706;19285!GO:0003715;transcription termination factor activity;0.023442419603706;19285!GO:0006361;transcription initiation from RNA polymerase I promoter;0.023442419603706;19285!GO:0006353;transcription termination;0.0252249413004837;19285!GO:0065003;macromolecular complex assembly;0.0252249413004837;77057,19285!GO:0016599;caveolar membrane;0.0252249413004837;19285!GO:0005901;caveola;0.0252249413004837;19285!GO:0006360;transcription from RNA polymerase I promoter;0.0252249413004837;19285!GO:0022607;cellular component assembly;0.0252249413004837;77057,19285!GO:0043624;cellular protein complex disassembly;0.0252249413004837;19285!GO:0043241;protein complex disassembly;0.0252249413004837;19285!GO:0032984;macromolecular complex disassembly;0.0252249413004837;19285!GO:0022411;cellular component disassembly;0.0325027641996785;19285!GO:0019843;rRNA binding;0.0325027641996785;19285!GO:0030119;AP-type membrane coat adaptor complex;0.0325027641996785;77057!GO:0030131;clathrin adaptor complex;0.0325027641996785;77057!GO:0006352;transcription initiation;0.0325027641996785;19285!GO:0030100;regulation of endocytosis;0.0397539599731975;77057!GO:0030118;clathrin 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|gostat_on_MCL_coexpression=GO:0042134;rRNA primary transcript binding;0.023442419603706;19285!GO:0003716;RNA polymerase I transcription termination factor activity;0.023442419603706;19285!GO:0003715;transcription termination factor activity;0.023442419603706;19285!GO:0006361;transcription initiation from RNA polymerase I promoter;0.023442419603706;19285!GO:0006353;transcription termination;0.0252249413004837;19285!GO:0065003;macromolecular complex assembly;0.0252249413004837;77057,19285!GO:0016599;caveolar membrane;0.0252249413004837;19285!GO:0005901;caveola;0.0252249413004837;19285!GO:0006360;transcription from RNA polymerase I promoter;0.0252249413004837;19285!GO:0022607;cellular component assembly;0.0252249413004837;77057,19285!GO:0043624;cellular protein complex disassembly;0.0252249413004837;19285!GO:0043241;protein complex disassembly;0.0252249413004837;19285!GO:0032984;macromolecular complex disassembly;0.0252249413004837;19285!GO:0022411;cellular component disassembly;0.0325027641996785;19285!GO:0019843;rRNA binding;0.0325027641996785;19285!GO:0030119;AP-type membrane coat adaptor complex;0.0325027641996785;77057!GO:0030131;clathrin adaptor complex;0.0325027641996785;77057!GO:0006352;transcription initiation;0.0325027641996785;19285!GO:0030100;regulation of endocytosis;0.0397539599731975;77057!GO:0030118;clathrin coat;0.0397539599731975;77057!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!1.91e-08!23;UBERON:0001009!1.91e-08!23;UBERON:0004872!6.65e-08!33;UBERON:0002048!1.34e-07!14;UBERON:0000117!1.34e-07!14;UBERON:0000171!1.34e-07!14;UBERON:0000170!1.34e-07!14;UBERON:0005597!1.34e-07!14;UBERON:0000118!1.34e-07!14;UBERON:0005157!2.81e-07!20
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.826837,1.34037,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.361892,0.374752,0.27937,0.598814,0.29769,1.07577,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.78719,0.498917,0.848378,0.468714,0.766323,0.57142,0.717242,0.652422,0.295233,0.507468,0.932136,0.317766,0.515031,0.469348,0.714592,0.532496,0.478447,0.347313,0.777641,0.654933,1.3744,1.04034,1.0579,0.606984,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.507615,0.159969,0.166511,0.703064,0.859987,1.75229,0.212973,0.812889,0.663039,0.200155,0.975495,1.37268,0.042613,1.41216,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,1.30733,0.237542,0.589174,0.913319,0.71485,1.29592,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,2.31879,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,1.81619,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,1.38961,1.04192,0.681896,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,3.44893
|tfbs_overrepresentation_jaspar=MA0003.1;4.19152,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;1.41063,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.860672,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;1.01509,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.801219,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;1.23731,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;6.79389,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;1.49527,MA0089.1;0,MA0090.1;4.00833,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.9471,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;1.56174,MA0146.1;0.792204,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.967192,MA0035.2;0.573016,MA0039.2;1.06357,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.957645,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;1.5617,MA0065.2;1.56466,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.687925,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.127623,MA0163.1;3.21163,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;7.96905,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:78054632..78054679,-p1@Syde1
Mm9::chr11:100831178..100831208,+p@chr11:100831178..100831208
+
Mm9::chr15:97661891..97661950,-p1@Hdac7
Mm9::chr17:88997003..88997044,+p1@Ston1
Mm9::chr18:60773155..60773181,-p@chr18:60773155..60773181
-
Mm9::chr18:60773184..60773212,-p@chr18:60773184..60773212
-
Mm9::chr1:191552143..191552205,+p1@Ptpn14


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:0042134rRNA primary transcript binding0.023442419603706
GO:0003716RNA polymerase I transcription termination factor activity0.023442419603706
GO:0003715transcription termination factor activity0.023442419603706
GO:0006361transcription initiation from RNA polymerase I promoter0.023442419603706
GO:0006353transcription termination0.0252249413004837
GO:0065003macromolecular complex assembly0.0252249413004837
GO:0016599caveolar membrane0.0252249413004837
GO:0005901caveola0.0252249413004837
GO:0006360transcription from RNA polymerase I promoter0.0252249413004837
GO:0022607cellular component assembly0.0252249413004837
GO:0043624cellular protein complex disassembly0.0252249413004837
GO:0043241protein complex disassembly0.0252249413004837
GO:0032984macromolecular complex disassembly0.0252249413004837
GO:0022411cellular component disassembly0.0325027641996785
GO:0019843rRNA binding0.0325027641996785
GO:0030119AP-type membrane coat adaptor complex0.0325027641996785
GO:0030131clathrin adaptor complex0.0325027641996785
GO:0006352transcription initiation0.0325027641996785
GO:0030100regulation of endocytosis0.0397539599731975
GO:0030118clathrin coat0.0397539599731975



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 system1.91e-0823
circulatory system1.91e-0823
splanchnic layer of lateral plate mesoderm6.65e-0833
lung1.34e-0714
respiratory tube1.34e-0714
respiration organ1.34e-0714
pair of lungs1.34e-0714
lung primordium1.34e-0714
lung bud1.34e-0714
epithelial fold2.81e-0720


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)
MA0003.14.19152
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.11.41063
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.11.01509
MA0043.11.02178
MA0046.10.960497
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.11.23731
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.16.79389
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.49527
MA0089.10
MA0090.14.00833
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.56174
MA0146.10.792204
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.967192
MA0035.20.573016
MA0039.21.06357
MA0138.20.727395
MA0002.20.592533
MA0137.20.957645
MA0104.20.218974
MA0047.20.626803
MA0112.21.5617
MA0065.21.56466
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.13.21163
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.27.96905
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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