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MCL coexpression mm9:1156: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002193!3.90e-14!48;UBERON:0002405!3.90e-14!48;UBERON:0002390!8.78e-13!45;UBERON:0003061!8.78e-13!45;UBERON:0002371!1.09e-10!16;UBERON:0001474!2.10e-10!22;UBERON:0004765!2.10e-10!22;UBERON:0001434!2.10e-10!22;UBERON:0002204!3.20e-08!32;UBERON:0003081!7.24e-08!87;UBERON:0000926!2.26e-07!120;UBERON:0004120!2.26e-07!120;UBERON:0006603!2.26e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,1.47084,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,1.40872,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,0.542568,0.516511,0.911169,0.145661,0.50223,0.897561,0.289148,0.166577,0.316253,0.248902,0.279977,0.57142,0.717242,1.89251,0.295233,0.507468,1.39631,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.200155,0.975495,0.0369809,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,1.40122,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,1.5026,1.00568,1.19218,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,1.48714,2.14328,1.40533,0.0206035
|tfbs_overrepresentation_jaspar=MA0003.1;0.188259,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,MA0017.1;0.337808,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;0.128106,MA0050.1;2.22815,MA0051.1;1.53797,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;1.33382,MA0063.1;0,MA0066.1;1.49567,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;13.8317,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;0.0841779,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;0.906859,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;1.04809,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;0.0910975,MA0146.1;0.0256827,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;0.573016,MA0039.2;0.113749,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.304722,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;1.25065,MA0161.1;0,MA0162.1;0.302441,MA0163.1;0.28052,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;1.47363,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:10511185..10511202,+p@chr17:10511185..10511202
+
Mm9::chr17:57418593..57418604,+p2@Vav1
Mm9::chr1:89537750..89537753,+p@chr1:89537750..89537753
+
Mm9::chr2:35318238..35318241,-p@chr2:35318238..35318241
-
Mm9::chr2:35318313..35318352,-p5@Ggta1
Mm9::chrX:83115605..83115636,+p1@5430427O19Rik
Mm9::chrX:83115663..83115674,+p3@5430427O19Rik


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:0047276N-acetyllactosaminide 3-alpha-galactosyltransferase activity0.015942584780584
GO:0030676Rac guanyl-nucleotide exchange factor activity0.0239112568070353



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
common myeloid progenitor5.82e-0819

Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.90e-1448
immune system3.90e-1448
hematopoietic system8.78e-1345
blood island8.78e-1345
bone marrow1.09e-1016
bone element2.10e-1022
skeletal element2.10e-1022
skeletal system2.10e-1022
musculoskeletal system3.20e-0832
lateral plate mesoderm7.24e-0887
mesoderm2.26e-07120
mesoderm-derived structure2.26e-07120
presumptive mesoderm2.26e-07120


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)
MA0003.10.188259
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
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
MA0048.10.128106
MA0050.12.22815
MA0051.11.53797
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.11.49567
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.113.8317
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
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
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
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
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.304722
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.11.25065
MA0161.10
MA0162.10.302441
MA0163.10.28052
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.21.47363
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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