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MCL coexpression mm9:946: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!3.68e-23!31;UBERON:0005409!1.42e-19!47;UBERON:0000344!3.46e-13!15;UBERON:0001242!1.19e-11!13;UBERON:0000060!1.19e-11!13;UBERON:0001262!1.19e-11!13;UBERON:0004786!1.19e-11!13;UBERON:0002113!4.12e-09!14;UBERON:0003918!4.12e-09!14;UBERON:0011143!4.12e-09!14;UBERON:0005095!4.12e-09!14;UBERON:0007687!4.12e-09!14;UBERON:0001008!1.43e-08!19;UBERON:0006554!2.05e-08!18;UBERON:0003350!3.23e-08!9;UBERON:0004808!3.23e-08!9;UBERON:0001277!3.23e-08!9;UBERON:0004923!3.35e-07!24
|ontology_enrichment_uberon=UBERON:0000160!3.68e-23!31;UBERON:0005409!1.42e-19!47;UBERON:0000344!3.46e-13!15;UBERON:0001242!1.19e-11!13;UBERON:0000060!1.19e-11!13;UBERON:0001262!1.19e-11!13;UBERON:0004786!1.19e-11!13;UBERON:0002113!4.12e-09!14;UBERON:0003918!4.12e-09!14;UBERON:0011143!4.12e-09!14;UBERON:0005095!4.12e-09!14;UBERON:0007687!4.12e-09!14;UBERON:0001008!1.43e-08!19;UBERON:0006554!2.05e-08!18;UBERON:0003350!3.23e-08!9;UBERON:0004808!3.23e-08!9;UBERON:0001277!3.23e-08!9;UBERON:0004923!3.35e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.938682,0.29826,0.332107,0.223663,0.549359,0.717658,0.978733,0.577606,0.466037,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.363049,0.242032,0.522578,0.631914,0.570041,0.256422,0.460258,0.784847,0.27776,0.403938,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,1.367,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,1.61056,0.759925,0.612313,0.167672,0.920903,0.263163,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.1711,0.859272,0.663249,1.12826,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.895335,1.24884,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,2.83289,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,1.03631,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.381863,0.0553085,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.842217
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.938682,0.29826,0.332107,0.223663,0.549359,0.717658,0.978733,0.577606,0.466037,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.363049,0.242032,0.522578,0.631914,0.570041,0.256422,0.460258,0.784847,0.27776,0.403938,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,1.367,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,1.61056,0.759925,0.612313,0.167672,0.920903,0.263163,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.1711,0.859272,0.663249,1.12826,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.895335,1.24884,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,2.83289,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,1.03631,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.381863,0.0553085,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.842217
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;3.09676,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;1.82653,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.282934,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.931383,MA0060.1;0.197678,MA0061.1;1.19505,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.00886773,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;1.74144,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.229377,MA0089.1;0,MA0090.1;1.03628,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;1.33477,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;2.60319,MA0115.1;0.969632,MA0116.1;0.747001,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;2.61335,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.246409,MA0146.1;0.385068,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.0706842,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.902537,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;2.3265,MA0154.1;1.12269,MA0155.1;0.978338,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0925951,MA0163.1;0.0836563,MA0164.1;1.35808,MA0080.2;1.48111,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.00265486,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:34, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:35055660..35055685,-p1@Eci3
Mm9::chr13:35055694..35055705,-p2@Eci3
Mm9::chr2:166885638..166885674,-p@chr2:166885638..166885674
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Mm9::chr4:137923796..137923807,-p@chr4:137923796..137923807
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Mm9::chr4:94316783..94316818,-p1@Lrrc19
Mm9::chr4:94316825..94316840,-p2@Lrrc19
Mm9::chr5:114454790..114454818,+p3@Dao
Mm9::chr9:107507434..107507453,-p@chr9:107507434..107507453
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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:0006551leucine metabolic process0.00905712736433923
GO:0003884D-amino-acid oxidase activity0.00905712736433923
GO:0046087cytidine metabolic process0.00905712736433923
GO:0046131pyrimidine ribonucleoside metabolic process0.0101884308949003
GO:0004126cytidine deaminase activity0.010866766470503
GO:0006213pyrimidine nucleoside metabolic process0.0118825956045149
GO:0009119ribonucleoside metabolic process0.0118825956045149
GO:0009081branched chain family amino acid metabolic process0.0118825956045149
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0237378594464625
GO:0009116nucleoside metabolic process0.0237378594464625
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0237378594464625
GO:0019239deaminase activity0.0237378594464625
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0239947699080005



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
intestinal epithelial cell3.23e-089
epithelial cell of alimentary canal3.23e-089

Uber Anatomy
Ontology termp-valuen
intestine3.68e-2331
gastrointestinal system1.42e-1947
mucosa3.46e-1315
intestinal mucosa1.19e-1113
anatomical wall1.19e-1113
wall of intestine1.19e-1113
gastrointestinal system mucosa1.19e-1113
kidney4.12e-0914
kidney mesenchyme4.12e-0914
upper urinary tract4.12e-0914
kidney rudiment4.12e-0914
kidney field4.12e-0914
renal system1.43e-0819
urinary system structure2.05e-0818
epithelium of mucosa3.23e-089
gastrointestinal system epithelium3.23e-089
intestinal epithelium3.23e-089
organ component layer3.35e-0724


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.13.09676
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.11.82653
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.931383
MA0060.10.197678
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00886773
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.11.74144
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.33477
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.12.60319
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.12.61335
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.385068
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.0706842
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.12.3265
MA0154.11.12269
MA0155.10.978338
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0925951
MA0163.10.0836563
MA0164.11.35808
MA0080.21.48111
MA0018.20.560731
MA0099.20.669311
MA0079.20.00265486
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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