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MCL coexpression mm9:1146: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002107!1.09e-17!22;UBERON:0007499!1.09e-17!22;UBERON:0006925!1.09e-17!22;UBERON:0009497!1.09e-17!22;UBERON:0000015!1.09e-17!22;UBERON:0002423!1.09e-17!22;UBERON:0006235!1.09e-17!22;UBERON:0008835!1.09e-17!22;UBERON:0003894!1.09e-17!22;UBERON:0004161!1.09e-17!22;UBERON:0008836!1.09e-17!22;UBERON:0009854!1.62e-16!23;UBERON:0009856!1.62e-16!23;UBERON:0000160!8.23e-16!31;UBERON:0005409!1.30e-15!47;UBERON:0002365!1.82e-14!25;UBERON:0002330!1.82e-14!25;UBERON:0001007!2.36e-13!116;UBERON:0001555!2.36e-13!116;UBERON:0007026!2.36e-13!116;UBERON:0001264!8.10e-13!12;UBERON:0004119!9.00e-13!118;UBERON:0000925!9.00e-13!118;UBERON:0006595!9.00e-13!118;UBERON:0004921!2.20e-12!114;UBERON:0005177!2.06e-10!79;UBERON:0000949!4.25e-09!72;UBERON:0005172!6.07e-08!49;UBERON:0005173!6.07e-08!49;UBERON:0002417!6.07e-08!49;UBERON:0000916!6.07e-08!49;UBERON:0000344!6.13e-08!15;UBERON:0000466!1.21e-07!79;UBERON:0002100!1.99e-07!90;UBERON:0003929!3.79e-07!55;UBERON:0002075!3.82e-07!19;UBERON:0001242!8.27e-07!13;UBERON:0000060!8.27e-07!13;UBERON:0001262!8.27e-07!13;UBERON:0004786!8.27e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,2.40707,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.731589,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,1.0368,1.28465,0.344372,0.145661,0.50223,0.897561,0.289148,1.53598,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.932136,0.317766,0.0275764,0.469348,0.714592,0.532496,0.478447,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.293368,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,1.59309,1.72681,0.975495,0.0369809,0.164297,2.03326,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.796976,0.187586,0.484437,0.796633,2.96403,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,2.47343,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0206035
|tfbs_overrepresentation_jaspar=MA0003.1;0.00513025,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0200028,MA0017.1;2.43592,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;2.00977,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;2.20556,MA0048.1;0.40238,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.117936,MA0058.1;1.00014,MA0059.1;0.397033,MA0060.1;1.22438,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;0.519509,MA0072.1;0.927016,MA0073.1;0.00782298,MA0074.1;0.580087,MA0076.1;0.938908,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;1.1347,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.879104,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;1.62423,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;2.04376,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;1.04809,MA0122.1;1.01209,MA0124.1;2.72676,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;1.3943,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;1.24416,MA0149.1;0.411562,MA0062.2;1.54019,MA0035.2;3.51662,MA0039.2;0.00226251,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;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;1.5176,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;6.36279e-07,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:22857564..22857578,-p2@Tbccd1
Mm9::chr1:138857048..138857071,-p2@Nr5a2
Mm9::chr1:138857076..138857105,-p1@Nr5a2
Mm9::chr1:138857112..138857130,-p7@Nr5a2
Mm9::chr1:89470591..89470607,+p1@Neu2
Mm9::chr4:119032487..119032502,-p6@Ccdc30
Mm9::chr4:119032505..119032522,-p5@Ccdc30


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:0008206bile acid metabolic process0.0325830935551571
GO:0042632cholesterol homeostasis0.0325830935551571
GO:0055088lipid homeostasis0.0325830935551571
GO:0055092sterol homeostasis0.0325830935551571



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
liver1.09e-1722
epithelial sac1.09e-1722
digestive gland1.09e-1722
epithelium of foregut-midgut junction1.09e-1722
anatomical boundary1.09e-1722
hepatobiliary system1.09e-1722
foregut-midgut junction1.09e-1722
hepatic diverticulum1.09e-1722
liver primordium1.09e-1722
septum transversum1.09e-1722
liver bud1.09e-1722
digestive tract diverticulum1.62e-1623
sac1.62e-1623
intestine8.23e-1631
gastrointestinal system1.30e-1547
exocrine gland1.82e-1425
exocrine system1.82e-1425
digestive system2.36e-13116
digestive tract2.36e-13116
primitive gut2.36e-13116
pancreas8.10e-1312
endoderm-derived structure9.00e-13118
endoderm9.00e-13118
presumptive endoderm9.00e-13118
subdivision of digestive tract2.20e-12114
trunk region element2.06e-1079
endocrine system4.25e-0972
abdomen element6.07e-0849
abdominal segment element6.07e-0849
abdominal segment of trunk6.07e-0849
abdomen6.07e-0849
mucosa6.13e-0815
immaterial anatomical entity1.21e-0779
trunk1.99e-0790
gut epithelium3.79e-0755
viscus3.82e-0719
intestinal mucosa8.27e-0713
anatomical wall8.27e-0713
wall of intestine8.27e-0713
gastrointestinal system mucosa8.27e-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)
MA0003.10.00513025
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0200028
MA0017.12.43592
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.12.00977
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.12.20556
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.117936
MA0058.11.00014
MA0059.10.397033
MA0060.11.22438
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00782298
MA0074.10.580087
MA0076.10.938908
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.11.62423
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.12.04376
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.12.72676
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.11.3943
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.21.54019
MA0035.23.51662
MA0039.20.00226251
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.304722
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.11.5176
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.26.36279e-07
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
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