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MCL coexpression mm9:1005: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005409!3.50e-13!47;UBERON:0004119!4.00e-13!118;UBERON:0000925!4.00e-13!118;UBERON:0006595!4.00e-13!118;UBERON:0001007!5.91e-13!116;UBERON:0001555!5.91e-13!116;UBERON:0007026!5.91e-13!116;UBERON:0004921!6.08e-12!114;UBERON:0000160!2.05e-10!31;UBERON:0004923!4.25e-10!24;UBERON:0000344!1.42e-08!15;UBERON:0001242!2.56e-07!13;UBERON:0000060!2.56e-07!13;UBERON:0001262!2.56e-07!13;UBERON:0004786!2.56e-07!13
|ontology_enrichment_uberon=UBERON:0005409!3.50e-13!47;UBERON:0004119!4.00e-13!118;UBERON:0000925!4.00e-13!118;UBERON:0006595!4.00e-13!118;UBERON:0001007!5.91e-13!116;UBERON:0001555!5.91e-13!116;UBERON:0007026!5.91e-13!116;UBERON:0004921!6.08e-12!114;UBERON:0000160!2.05e-10!31;UBERON:0004923!4.25e-10!24;UBERON:0000344!1.42e-08!15;UBERON:0001242!2.56e-07!13;UBERON:0000060!2.56e-07!13;UBERON:0001262!2.56e-07!13;UBERON:0004786!2.56e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.45672,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.616096,0.478312,0.542749,1.40872,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.112498,0.978328,0.988929,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,1.25421,0.897561,0.289148,0.964228,0.316253,0.248902,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.82704,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.507615,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.146394,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,0.573477,1.03935
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.45672,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.616096,0.478312,0.542749,1.40872,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.112498,0.978328,0.988929,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,1.25421,0.897561,0.289148,0.964228,0.316253,0.248902,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.82704,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.507615,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.146394,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,0.573477,1.03935
|tfbs_overrepresentation_jaspar=MA0003.1;0.0286946,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;2.13157,MA0014.1;1.02494,MA0017.1;0.89657,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;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;1.33382,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;0.655058,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.89377,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;1.00582,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.84519,MA0103.1;0.348572,MA0105.1;0.9471,MA0106.1;1.62423,MA0107.1;2.45837,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;1.51389,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;0.72625,MA0145.1;0.0910975,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;2.93496,MA0035.2;0.573016,MA0039.2;2.09945,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.631649,MA0065.2;0.0914071,MA0150.1;1.17631,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.55478,MA0163.1;0.82914,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.86982,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.729797,MA0442.1;0
}}
}}

Revision as of 12:39, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:10277929..10277988,-p1@Rab32
Mm9::chr7:19470028..19470058,+p1@Pglyrp1
Mm9::chr7:19475704..19475720,-p@chr7:19475704..19475720
-
Mm9::chr7:19475766..19475773,-p@chr7:19475766..19475773
-
Mm9::chr7:38968666..38968687,+p4@1600014C10Rik
Mm9::chr7:38968823..38968888,+p1@1600014C10Rik
Mm9::chrX:35988243..35988270,-p2@C1galt1c1


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:0016019peptidoglycan receptor activity0.0188384740196361
GO:0042834peptidoglycan binding0.0188384740196361
GO:0008329pattern recognition receptor activity0.0188384740196361
GO:0008745N-acetylmuramoyl-L-alanine amidase activity0.0188384740196361
GO:0009253peptidoglycan catabolic process0.0188384740196361
GO:0000270peptidoglycan metabolic process0.0188384740196361



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 system3.50e-1347
endoderm-derived structure4.00e-13118
endoderm4.00e-13118
presumptive endoderm4.00e-13118
digestive system5.91e-13116
digestive tract5.91e-13116
primitive gut5.91e-13116
subdivision of digestive tract6.08e-12114
intestine2.05e-1031
organ component layer4.25e-1024
mucosa1.42e-0815
intestinal mucosa2.56e-0713
anatomical wall2.56e-0713
wall of intestine2.56e-0713
gastrointestinal system mucosa2.56e-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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.12.13157
MA0014.11.02494
MA0017.10.89657
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
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.655058
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.89377
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.00582
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.84519
MA0103.10.348572
MA0105.10.9471
MA0106.11.62423
MA0107.12.45837
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.11.51389
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
MA0144.10.72625
MA0145.10.0910975
MA0146.10.264322
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.22.93496
MA0035.20.573016
MA0039.22.09945
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.631649
MA0065.20.0914071
MA0150.11.17631
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.55478
MA0163.10.82914
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.20.86982
MA0102.21.65195
MA0258.10.688848
MA0259.10.729797
MA0442.10
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