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MCL coexpression mm9:789: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0045062;extrathymic T cell selection;0.0167780638799102;16168!GO:0050691;regulation of defense response to virus by host;0.0167780638799102;16168!GO:0008892;guanine deaminase activity;0.0167780638799102;14544!GO:0033078;extrathymic T cell differentiation;0.0167780638799102;16168!GO:0003708;retinoic acid receptor activity;0.0191717784505482;19401!GO:0050688;regulation of defense response to virus;0.0191717784505482;16168!GO:0001866;NK T cell proliferation;0.0191717784505482;16168!GO:0004030;aldehyde dehydrogenase [NAD(P)+] activity;0.041917589897169;11671!GO:0055012;ventricular cardiac muscle cell differentiation;0.0447047472996375;19401!GO:0004029;aldehyde dehydrogenase (NAD) activity;0.0469322700537544;11671!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!3.56e-13!47;UBERON:0000160!5.49e-13!31;UBERON:0004119!8.61e-10!118;UBERON:0000925!8.61e-10!118;UBERON:0006595!8.61e-10!118;UBERON:0007023!1.30e-09!51;UBERON:0001007!2.72e-09!116;UBERON:0001555!2.72e-09!116;UBERON:0007026!2.72e-09!116;UBERON:0004921!1.58e-08!114;UBERON:0000344!8.14e-08!15;UBERON:0004923!8.44e-08!24;UBERON:0001242!8.97e-07!13;UBERON:0000060!8.97e-07!13;UBERON:0001262!8.97e-07!13;UBERON:0004786!8.97e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.468136,0.573183,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.419123,0.902262,0.296085,0.403891,0.50668,0.64218,0.337218,0.534339,1.30297,0.428336,0.739731,1.09271,1.06602,0.796599,0.624261,0.364174,2.74163,0.137663,0.210533,0.480503,0.191662,0.967553,0.224094,0.419787,0.163087,0.244285,0.536558,0.383899,0.618203,0.443479,0.133514,0.745859,0.679429,0.560572,0.0915709,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,1.51902,0.460931,0.191038,0.987652,0.371787,0.710896,0.364033,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.967095,0.231102,0.0965007,0.623015,1.60001,1.15927,2.03711,0.809272,0.232894,0.551605,0.17334,0.444003,0.812053,0.618454,0.0816605,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,1.74861,0.439611,0.30446,1.46548,0.348012,0.921485,0.301014,0.458194,1.16629,0.633313,0.265919,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,0.161645,0.938577,1.01208,0.526881,1.01974,1.38016,0.253271,0.352329,0.362302,2.58709,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.976805
}}

Latest revision as of 15:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:61080643..61080656,-p2@Aldh3a2
Mm9::chr11:98822047..98822072,+p9@Rara
Mm9::chr16:93712197..93712253,+p1@Dopey2
Mm9::chr19:21547042..21547096,-p1@Gda
Mm9::chr2:29643002..29643031,+p5@Coq4
Mm9::chr2:29643841..29643855,+p2@Coq4
Mm9::chr4:43591581..43591644,+p2@Rgp1
Mm9::chr4:45985209..45985237,+p1@Tdrd7
Mm9::chr8:84927102..84927126,-p1@Il15


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:0045062extrathymic T cell selection0.0167780638799102
GO:0050691regulation of defense response to virus by host0.0167780638799102
GO:0008892guanine deaminase activity0.0167780638799102
GO:0033078extrathymic T cell differentiation0.0167780638799102
GO:0003708retinoic acid receptor activity0.0191717784505482
GO:0050688regulation of defense response to virus0.0191717784505482
GO:0001866NK T cell proliferation0.0191717784505482
GO:0004030aldehyde dehydrogenase [NAD(P)+] activity0.041917589897169
GO:0055012ventricular cardiac muscle cell differentiation0.0447047472996375
GO:0004029aldehyde dehydrogenase (NAD) activity0.0469322700537544



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 system3.56e-1347
intestine5.49e-1331
endoderm-derived structure8.61e-10118
endoderm8.61e-10118
presumptive endoderm8.61e-10118
adult organism1.30e-0951
digestive system2.72e-09116
digestive tract2.72e-09116
primitive gut2.72e-09116
subdivision of digestive tract1.58e-08114
mucosa8.14e-0815
organ component layer8.44e-0824
intestinal mucosa8.97e-0713
anatomical wall8.97e-0713
wall of intestine8.97e-0713
gastrointestinal system mucosa8.97e-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)
MA0003.11.1827
MA0004.11.02263
MA0006.11.24699
MA0007.10.38073
MA0009.10.82278
MA0014.10.961396
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.865043
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.11.10321
MA0051.10.542972
MA0052.10.84317
MA0055.11.4071
MA0056.10
MA0057.10.0745664
MA0058.11.49242
MA0059.10.849123
MA0060.10.505012
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0771206
MA0074.11.22546
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.867731
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.867077
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.200183
MA0146.11.46813
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.20.365726
MA0035.20.482026
MA0039.24.07545
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.200175
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.875406
MA0163.10.820439
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.670082
MA0102.21.5442
MA0258.10.533988
MA0259.11.08444
MA0442.10
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