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MCL coexpression mm9:661: Difference between revisions

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{{MCL_coexpression_mm9
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dehydrogenase activity;0.0363566590794229;98711!GO:0005041;low-density lipoprotein receptor activity;0.0363566590794229;66102!GO:0030169;low-density lipoprotein binding;0.0363566590794229;66102!GO:0030228;lipoprotein receptor activity;0.0363566590794229;66102!GO:0008034;lipoprotein binding;0.041451227913054;66102!GO:0009605;response to external stimulus;0.041451227913054;16420,66102!GO:0005178;integrin binding;0.041451227913054;16420!GO:0005605;basal lamina;0.041451227913054;16780!GO:0005044;scavenger receptor activity;0.041451227913054;66102!GO:0022610;biological adhesion;0.041451227913054;16420,16780!GO:0007155;cell adhesion;0.041451227913054;16420,16780!GO:0005102;receptor binding;0.041451227913054;16420,66102!GO:0008305;integrin complex;0.045938341315148;16420!GO:0008009;chemokine activity;0.045938341315148;66102!GO:0042379;chemokine receptor 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|gostat_on_MCL_coexpression=GO:0004745;retinol dehydrogenase activity;0.0363566590794229;98711!GO:0005041;low-density lipoprotein receptor activity;0.0363566590794229;66102!GO:0030169;low-density lipoprotein binding;0.0363566590794229;66102!GO:0030228;lipoprotein receptor activity;0.0363566590794229;66102!GO:0008034;lipoprotein binding;0.041451227913054;66102!GO:0009605;response to external stimulus;0.041451227913054;16420,66102!GO:0005178;integrin binding;0.041451227913054;16420!GO:0005605;basal lamina;0.041451227913054;16780!GO:0005044;scavenger receptor activity;0.041451227913054;66102!GO:0022610;biological adhesion;0.041451227913054;16420,16780!GO:0007155;cell adhesion;0.041451227913054;16420,16780!GO:0005102;receptor binding;0.041451227913054;16420,66102!GO:0008305;integrin complex;0.045938341315148;16420!GO:0008009;chemokine activity;0.045938341315148;66102!GO:0042379;chemokine receptor binding;0.045938341315148;66102!
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|ontology_enrichment_uberon=UBERON:0004119!4.63e-18!118;UBERON:0000925!4.63e-18!118;UBERON:0006595!4.63e-18!118;UBERON:0001007!1.58e-17!116;UBERON:0001555!1.58e-17!116;UBERON:0007026!1.58e-17!116;UBERON:0004921!3.13e-16!114;UBERON:0000160!5.26e-13!31;UBERON:0005409!6.04e-13!47;UBERON:0000344!1.64e-09!15;UBERON:0001242!4.96e-08!13;UBERON:0000060!4.96e-08!13;UBERON:0001262!4.96e-08!13;UBERON:0004786!4.96e-08!13;UBERON:0004923!7.80e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.750994,0.269904,0.878892,0.176699,0.342839,0.425757,0.345089,0.112618,0.208174,0.385334,0.414631,0.106288,0.437133,0.555819,0,0.619876,0.170475,0.096222,0.387499,0.670854,0.281622,0.436294,0.520732,0.758244,0.4628,0.630402,0.361771,0.611503,0.500344,0.349031,0.717576,0.504188,0.570676,0.19035,0.732568,0.161521,0.411296,0.873942,0.123934,0.173534,0.353696,0.255102,0.191571,1.11259,0.319944,1.34233,0.376103,0.081888,0.61724,0.603113,0.488021,0.220536,0.855661,0.87275,1.12875,0.634658,0.40287,0.288386,0.441884,0.698157,0.496904,0.769309,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.0307733,0.905636,0.0810502,0.932285,1.98595,0.532872,0.681539,0.242107,0.357936,0.636582,0.495545,0.101814,0.792744,0.0439644,0.0106044,1.29984,0.548334,1.51408,1.07554,0.797601,0.730003,1.02436,0.141946,0.404817,1.14799,0.732731,0.543917,0.197581,0.486605,0.717305,0.838603,1.4689,0.602672,0.353298,0.660145,0.372438,0.246223,0.67437,0.781068,0.840348,0.681364,0.390066,1.0825,2.23729,0.170188,0.333247,0.621127,0.158673,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,1.55739,0.976125,0.456508,1.10385,0.514451,0.811774,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.235808,0.0240729,0.857198,0.824171,1.15434,0.93735,1.22588,0.57908,0.290467,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,0.413167,0.671583
|tfbs_overrepresentation_jaspar=MA0003.1;0.156602,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;1.75966,MA0014.1;0.270116,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.567414,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.054097,MA0050.1;1.70452,MA0051.1;3.0609,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;0.048013,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;1.42191,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.0394021,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;1.39097,MA0083.1;1.95254,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.849797,MA0089.1;0,MA0090.1;2.24963,MA0091.1;0.342071,MA0092.1;1.47462,MA0093.1;0.58345,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;2.07249,MA0103.1;0.216742,MA0105.1;0.94454,MA0106.1;1.26962,MA0107.1;1.79018,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;2.89303,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.338099,MA0140.1;0.408417,MA0141.1;1.90558,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.3137,MA0146.1;0.775515,MA0147.1;0.925698,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;1.65335,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.652494,MA0104.2;0.744492,MA0047.2;0.46201,MA0112.2;0.313687,MA0065.2;0.033123,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;1.16232,MA0155.1;0.154271,MA0156.1;0.634231,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.103104,MA0163.1;0.0308606,MA0164.1;0.437937,MA0080.2;1.14688,MA0018.2;1.98396,MA0099.2;0.549696,MA0079.2;0.34501,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.455671,MA0442.1;0
}}

Latest revision as of 15:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70272314..70272350,-p@chr11:70272314..70272350
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Mm9::chr11:70273427..70273451,-p4@Cxcl16
Mm9::chr11:70273459..70273486,-p3@Cxcl16
Mm9::chr11:70273488..70273503,-p6@Cxcl16
Mm9::chr1:16095475..16095491,+p1@Rdh10
Mm9::chr1:195128229..195128241,+p5@Lamb3
Mm9::chr1:195128260..195128276,+p1@Lamb3
Mm9::chr2:157202181..157202186,-p@chr2:157202181..157202186
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Mm9::chr2:60511711..60511788,-p1@Itgb6
Mm9::chr4:123465100..123465129,+p1@Rhbdl2
Mm9::chr7:108696379..108696386,+p@chr7:108696379..108696386
+


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:0004745retinol dehydrogenase activity0.0363566590794229
GO:0005041low-density lipoprotein receptor activity0.0363566590794229
GO:0030169low-density lipoprotein binding0.0363566590794229
GO:0030228lipoprotein receptor activity0.0363566590794229
GO:0008034lipoprotein binding0.041451227913054
GO:0009605response to external stimulus0.041451227913054
GO:0005178integrin binding0.041451227913054
GO:0005605basal lamina0.041451227913054
GO:0005044scavenger receptor activity0.041451227913054
GO:0022610biological adhesion0.041451227913054
GO:0007155cell adhesion0.041451227913054
GO:0005102receptor binding0.041451227913054
GO:0008305integrin complex0.045938341315148
GO:0008009chemokine activity0.045938341315148
GO:0042379chemokine receptor binding0.045938341315148



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
endoderm-derived structure4.63e-18118
endoderm4.63e-18118
presumptive endoderm4.63e-18118
digestive system1.58e-17116
digestive tract1.58e-17116
primitive gut1.58e-17116
subdivision of digestive tract3.13e-16114
intestine5.26e-1331
gastrointestinal system6.04e-1347
mucosa1.64e-0915
intestinal mucosa4.96e-0813
anatomical wall4.96e-0813
wall of intestine4.96e-0813
gastrointestinal system mucosa4.96e-0813
organ component layer7.80e-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)
MA0003.10.156602
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.11.75966
MA0014.10.270116
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.567414
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.054097
MA0050.11.70452
MA0051.13.0609
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.10.048013
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.11.42191
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0394021
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.11.39097
MA0083.11.95254
MA0084.11.4063
MA0087.10.794721
MA0088.10.849797
MA0089.10
MA0090.12.24963
MA0091.10.342071
MA0092.11.47462
MA0093.10.58345
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.12.07249
MA0103.10.216742
MA0105.10.94454
MA0106.11.26962
MA0107.11.79018
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.12.89303
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.338099
MA0140.10.408417
MA0141.11.90558
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.3137
MA0146.10.775515
MA0147.10.925698
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.20.412747
MA0039.21.65335
MA0138.20.555696
MA0002.20.105469
MA0137.20.652494
MA0104.20.744492
MA0047.20.46201
MA0112.20.313687
MA0065.20.033123
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.11.16232
MA0155.10.154271
MA0156.10.634231
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.103104
MA0163.10.0308606
MA0164.10.437937
MA0080.21.14688
MA0018.21.98396
MA0099.20.549696
MA0079.20.34501
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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