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MCL coexpression mm9:953: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002100!1.22e-14!90;UBERON:0005177!8.06e-13!79;UBERON:0004119!9.35e-12!118;UBERON:0000925!9.35e-12!118;UBERON:0006595!9.35e-12!118;UBERON:0001007!7.99e-11!116;UBERON:0001555!7.99e-11!116;UBERON:0007026!7.99e-11!116;UBERON:0005256!1.06e-10!45;UBERON:0000466!1.17e-10!79;UBERON:0002365!2.49e-10!25;UBERON:0002330!2.49e-10!25;UBERON:0004921!4.05e-10!114;UBERON:0005409!2.45e-09!47;UBERON:0000160!4.41e-09!31;UBERON:0009854!4.89e-09!23;UBERON:0009856!4.89e-09!23;UBERON:0002107!9.48e-09!22;UBERON:0007499!9.48e-09!22;UBERON:0006925!9.48e-09!22;UBERON:0009497!9.48e-09!22;UBERON:0000015!9.48e-09!22;UBERON:0002423!9.48e-09!22;UBERON:0006235!9.48e-09!22;UBERON:0008835!9.48e-09!22;UBERON:0003894!9.48e-09!22;UBERON:0004161!9.48e-09!22;UBERON:0008836!9.48e-09!22;UBERON:0003104!2.32e-08!61;UBERON:0009142!2.32e-08!61;UBERON:0001264!4.15e-08!12;UBERON:0009569!1.62e-07!66;UBERON:0005172!6.19e-07!49;UBERON:0005173!6.19e-07!49;UBERON:0002417!6.19e-07!49;UBERON:0000916!6.19e-07!49
|ontology_enrichment_uberon=UBERON:0002100!1.22e-14!90;UBERON:0005177!8.06e-13!79;UBERON:0004119!9.35e-12!118;UBERON:0000925!9.35e-12!118;UBERON:0006595!9.35e-12!118;UBERON:0001007!7.99e-11!116;UBERON:0001555!7.99e-11!116;UBERON:0007026!7.99e-11!116;UBERON:0005256!1.06e-10!45;UBERON:0000466!1.17e-10!79;UBERON:0002365!2.49e-10!25;UBERON:0002330!2.49e-10!25;UBERON:0004921!4.05e-10!114;UBERON:0005409!2.45e-09!47;UBERON:0000160!4.41e-09!31;UBERON:0009854!4.89e-09!23;UBERON:0009856!4.89e-09!23;UBERON:0002107!9.48e-09!22;UBERON:0007499!9.48e-09!22;UBERON:0006925!9.48e-09!22;UBERON:0009497!9.48e-09!22;UBERON:0000015!9.48e-09!22;UBERON:0002423!9.48e-09!22;UBERON:0006235!9.48e-09!22;UBERON:0008835!9.48e-09!22;UBERON:0003894!9.48e-09!22;UBERON:0004161!9.48e-09!22;UBERON:0008836!9.48e-09!22;UBERON:0003104!2.32e-08!61;UBERON:0009142!2.32e-08!61;UBERON:0001264!4.15e-08!12;UBERON:0009569!1.62e-07!66;UBERON:0005172!6.19e-07!49;UBERON:0005173!6.19e-07!49;UBERON:0002417!6.19e-07!49;UBERON:0000916!6.19e-07!49
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.386846,0.494602,0.526159,1.57591,1.35627,0.275867,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.136998,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.256422,1.16427,0.204736,0.27776,0.663502,0.423266,0.662995,1.21655,0.170971,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,1.78254,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.872563,1.03623,1.37807,0.813951,0.42492,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.501608,0.920903,0.789543,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,1.82579,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.946242,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,1.82213,1.19035,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,0.524587,0.331912
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.386846,0.494602,0.526159,1.57591,1.35627,0.275867,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.136998,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.256422,1.16427,0.204736,0.27776,0.663502,0.423266,0.662995,1.21655,0.170971,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,1.78254,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.872563,1.03623,1.37807,0.813951,0.42492,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.501608,0.920903,0.789543,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,1.82579,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.946242,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,1.82213,1.19035,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,0.524587,0.331912
|tfbs_overrepresentation_jaspar=MA0003.1;0.848341,MA0004.1;1.10905,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,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;1.66702,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.90507,MA0059.1;0.353484,MA0060.1;4.06358,MA0061.1;0.224905,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;0.845594,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.853781,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;1.43515,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,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;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,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;0.977634,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.900473,MA0146.1;0.636109,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,MA0035.2;0.524137,MA0039.2;0.812684,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.0804339,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.439322,MA0163.1;0.212034,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0468707,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:34, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:119337147..119337214,+p1@Dnajc3
Mm9::chr14:73002752..73002810,-p2@Fndc3a
Mm9::chr1:36300977..36301021,-p2@Uggt1
Mm9::chr4:48292416..48292485,-p1@Erp44
Mm9::chr6:47746242..47746246,-p@chr6:47746242..47746246
-
Mm9::chr9:106794239..106794251,-p2@Manf
Mm9::chr9:44187619..44187707,+p1@Hyou1
Mm9::chr9:44200284..44200288,+p@chr9:44200284..44200288
+


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:0006986response to unfolded protein0.000760466938137463
GO:0051789response to protein stimulus0.000760466938137463
GO:0005783endoplasmic reticulum0.00578683079327287
GO:0006950response to stress0.00578683079327287
GO:0009607response to biotic stimulus0.0119287071954611
GO:0044444cytoplasmic part0.0119287071954611
GO:0005788endoplasmic reticulum lumen0.022777665929277
GO:0042221response to chemical stimulus0.0354537894644572
GO:0004860protein kinase inhibitor activity0.0382727595647032
GO:0005615extracellular space0.0382727595647032
GO:0019210kinase inhibitor activity0.0382727595647032
GO:0001669acrosome0.0382727595647032
GO:0044421extracellular region part0.0382727595647032
GO:0005737cytoplasm0.0423176696192316
GO:0006469negative regulation of protein kinase activity0.0423176696192316
GO:0033673negative regulation of kinase activity0.0423176696192316
GO:0051348negative regulation of transferase activity0.0423176696192316
GO:0045454cell redox homeostasis0.0423176696192316
GO:0007286spermatid development0.0423176696192316
GO:0048515spermatid differentiation0.0423176696192316
GO:0043086negative regulation of catalytic activity0.0423176696192316
GO:0031072heat shock protein binding0.0423176696192316
GO:0009566fertilization0.0423176696192316
GO:0012506vesicle membrane0.0462945999488851
GO:0043231intracellular membrane-bound organelle0.0462945999488851
GO:0043227membrane-bound organelle0.0462945999488851
GO:0019887protein kinase regulator activity0.0462945999488851



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
epithelial cell2.27e-0725

Uber Anatomy
Ontology termp-valuen
trunk1.22e-1490
trunk region element8.06e-1379
endoderm-derived structure9.35e-12118
endoderm9.35e-12118
presumptive endoderm9.35e-12118
digestive system7.99e-11116
digestive tract7.99e-11116
primitive gut7.99e-11116
trunk mesenchyme1.06e-1045
immaterial anatomical entity1.17e-1079
exocrine gland2.49e-1025
exocrine system2.49e-1025
subdivision of digestive tract4.05e-10114
gastrointestinal system2.45e-0947
intestine4.41e-0931
digestive tract diverticulum4.89e-0923
sac4.89e-0923
liver9.48e-0922
epithelial sac9.48e-0922
digestive gland9.48e-0922
epithelium of foregut-midgut junction9.48e-0922
anatomical boundary9.48e-0922
hepatobiliary system9.48e-0922
foregut-midgut junction9.48e-0922
hepatic diverticulum9.48e-0922
liver primordium9.48e-0922
septum transversum9.48e-0922
liver bud9.48e-0922
mesenchyme2.32e-0861
entire embryonic mesenchyme2.32e-0861
pancreas4.15e-0812
subdivision of trunk1.62e-0766
abdomen element6.19e-0749
abdominal segment element6.19e-0749
abdominal segment of trunk6.19e-0749
abdomen6.19e-0749


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)
MA0003.10.848341
MA0004.11.10905
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.11.66702
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.0935008
MA0058.10.90507
MA0059.10.353484
MA0060.14.06358
MA0061.10.224905
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
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.11.43515
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.900473
MA0146.10.636109
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.20.812684
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.439322
MA0163.10.212034
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0468707
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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