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MCL coexpression mm9:1064: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!4.69e-13!31;UBERON:0005409!4.41e-11!47;UBERON:0000344!1.77e-08!15;UBERON:0001242!1.87e-07!13;UBERON:0000060!1.87e-07!13;UBERON:0001262!1.87e-07!13;UBERON:0004786!1.87e-07!13
|ontology_enrichment_uberon=UBERON:0000160!4.69e-13!31;UBERON:0005409!4.41e-11!47;UBERON:0000344!1.77e-08!15;UBERON:0001242!1.87e-07!13;UBERON:0000060!1.87e-07!13;UBERON:0001262!1.87e-07!13;UBERON:0004786!1.87e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.219671,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,1.68259,1.75604,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,0.446946,0.50223,0.897561,0.78719,0.166577,0.316253,0.101236,0.766323,0.57142,0.258564,0.652422,0.295233,0.507468,0.0742755,0.317766,0.277561,0.469348,0.714592,0.532496,0.0609361,1.64197,0.777641,0.654933,0.431711,1.04034,1.0579,1.47583,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.02583,1.09164,0.97874,1.49715,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.960306,0.042613,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.589174,0.913319,0.71485,0.127063,0.7665,2.07642,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.813943,2.05013,1.38961,1.04192,1.26486,0.619892,1.12411,0.655955,1.57287,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,2.88237
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.219671,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,1.68259,1.75604,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,0.446946,0.50223,0.897561,0.78719,0.166577,0.316253,0.101236,0.766323,0.57142,0.258564,0.652422,0.295233,0.507468,0.0742755,0.317766,0.277561,0.469348,0.714592,0.532496,0.0609361,1.64197,0.777641,0.654933,0.431711,1.04034,1.0579,1.47583,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.02583,1.09164,0.97874,1.49715,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.960306,0.042613,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.589174,0.913319,0.71485,0.127063,0.7665,2.07642,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.813943,2.05013,1.38961,1.04192,1.26486,0.619892,1.12411,0.655955,1.57287,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,2.88237
|tfbs_overrepresentation_jaspar=MA0003.1;2.21402,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;1.41063,MA0017.1;1.60852,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,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;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;1.8892,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.756125,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;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;1.29103,MA0072.1;0.927016,MA0073.1;0.00782298,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;1.13539,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,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;2.85274,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;2.46038,MA0140.1;0.568252,MA0141.1;1.71513,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;1.56174,MA0146.1;1.15352,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;0.573016,MA0039.2;2.09945,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;3.47073,MA0065.2;1.0577,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;1.4173,MA0160.1;0.50056,MA0161.1;0,MA0162.1;2.75316,MA0163.1;0.519779,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;3.13697,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
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Revision as of 12:45, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:121563707..121563718,+p3@Metrnl
Mm9::chr11:121563732..121563748,+p1@Metrnl
Mm9::chr11:121563767..121563781,+p2@Metrnl
Mm9::chr19:4269140..4269200,-p1@Ssh3
Mm9::chr2:160192793..160192809,-p1@Mafb
Mm9::chr4:141430794..141430868,-p1@Efhd2
Mm9::chr8:118231350..118231385,-p7@Maf


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:0045944positive regulation of transcription from RNA polymerase II promoter0.0294313341529811
GO:0046983protein dimerization activity0.0294313341529811
GO:0045893positive regulation of transcription, DNA-dependent0.0294313341529811
GO:0045941positive regulation of transcription0.0294313341529811
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0294313341529811
GO:0007379segment specification0.0294313341529811
GO:0031325positive regulation of cellular metabolic process0.0294313341529811
GO:0009893positive regulation of metabolic process0.0294313341529811
GO:0006357regulation of transcription from RNA polymerase II promoter0.0294313341529811
GO:0006366transcription from RNA polymerase II promoter0.0304484986597984
GO:0043565sequence-specific DNA binding0.0304484986597984
GO:0007585respiratory gaseous exchange0.0363785067069221



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
intestine4.69e-1331
gastrointestinal system4.41e-1147
mucosa1.77e-0815
intestinal mucosa1.87e-0713
anatomical wall1.87e-0713
wall of intestine1.87e-0713
gastrointestinal system mucosa1.87e-0713


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)
MA0003.12.21402
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.11.41063
MA0017.11.60852
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.11.8892
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.756125
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.11.29103
MA0072.10.927016
MA0073.10.00782298
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.11.13539
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.12.85274
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
MA0139.12.46038
MA0140.10.568252
MA0141.11.71513
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.56174
MA0146.11.15352
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.22.09945
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.21.17226
MA0047.20.626803
MA0112.23.47073
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.11.4173
MA0160.10.50056
MA0161.10
MA0162.12.75316
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.23.13697
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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