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MCL coexpression mm9:658: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000065!1.99e-08!41;UBERON:0001004!4.80e-08!42;UBERON:0005178!1.80e-07!17;UBERON:0005181!1.80e-07!17;UBERON:0002224!1.80e-07!17;UBERON:0000915!1.80e-07!17;UBERON:0008947!1.80e-07!17;UBERON:0003258!1.80e-07!17
|ontology_enrichment_uberon=UBERON:0000065!1.99e-08!41;UBERON:0001004!4.80e-08!42;UBERON:0005178!1.80e-07!17;UBERON:0005181!1.80e-07!17;UBERON:0002224!1.80e-07!17;UBERON:0000915!1.80e-07!17;UBERON:0008947!1.80e-07!17;UBERON:0003258!1.80e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.286791,0.7433,0.329881,0.52369,0.342839,0.425757,0.106126,0.732132,0.401738,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.096222,0.387499,0.238546,0.831639,0.436294,1.00057,0.276437,0.4628,0.630402,0.361771,1.79888,0.0650265,0.349031,0.717576,0.168723,0.270473,0.19035,0.308746,0.161521,0.411296,0.445168,1.27598,0.51597,0.353696,0.770976,1.06512,1.11259,0.319944,0.543674,0.376103,0.97944,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.634658,0.40287,0.60268,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.706068,0.355763,0.299271,0.905636,0.0810502,1.39651,0.570456,0.532872,0.681539,0.679143,0.724739,0.636582,1.23994,0.101814,0.792744,0.00855221,0.0106044,0.231893,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.404817,0.694736,0.732731,0.543917,1.16887,0.943642,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.479408,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,2.88779,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.2772,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.816464,0.527071,0.235808,0.0240729,0.857198,0.824171,0.455644,0.93735,0.488969,0.57908,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,2.14982,0.413167,0.148813
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.286791,0.7433,0.329881,0.52369,0.342839,0.425757,0.106126,0.732132,0.401738,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.096222,0.387499,0.238546,0.831639,0.436294,1.00057,0.276437,0.4628,0.630402,0.361771,1.79888,0.0650265,0.349031,0.717576,0.168723,0.270473,0.19035,0.308746,0.161521,0.411296,0.445168,1.27598,0.51597,0.353696,0.770976,1.06512,1.11259,0.319944,0.543674,0.376103,0.97944,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.634658,0.40287,0.60268,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.706068,0.355763,0.299271,0.905636,0.0810502,1.39651,0.570456,0.532872,0.681539,0.679143,0.724739,0.636582,1.23994,0.101814,0.792744,0.00855221,0.0106044,0.231893,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.404817,0.694736,0.732731,0.543917,1.16887,0.943642,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.479408,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,2.88779,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.2772,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.816464,0.527071,0.235808,0.0240729,0.857198,0.824171,0.455644,0.93735,0.488969,0.57908,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,2.14982,0.413167,0.148813
|tfbs_overrepresentation_jaspar=MA0003.1;0.0374387,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;1.56158,MA0017.1;0.207884,MA0019.1;1.39291,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,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;0.769903,MA0050.1;0.365212,MA0051.1;1.18756,MA0052.1;0.76328,MA0055.1;0.136328,MA0056.1;0,MA0057.1;0.71676,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;2.04604,MA0063.1;0,MA0066.1;1.1475,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.0103656,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.534411,MA0089.1;0,MA0090.1;2.24963,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;1.05226,MA0101.1;0.73212,MA0103.1;1.16365,MA0105.1;1.95127,MA0106.1;0.509454,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;1.34784,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;1.11539,MA0139.1;0.103495,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.452699,MA0145.1;0.903527,MA0146.1;0.331601,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;0.675078,MA0138.2;0.555696,MA0002.2;0.343346,MA0137.2;0.230686,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.133279,MA0065.2;0.033123,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.434137,MA0155.1;0.637282,MA0156.1;1.851,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.957875,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.00661648,MA0163.1;0.0308606,MA0164.1;0.437937,MA0080.2;1.14688,MA0018.2;0.446948,MA0099.2;1.35508,MA0079.2;0.534138,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.14914,MA0442.1;0
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Revision as of 12:06, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:67345950..67345978,+p@chr11:67345950..67345978
+
Mm9::chr18:83996995..83997000,-p@chr18:83996995..83997000
-
Mm9::chr1:95056844..95056862,-p@chr1:95056844..95056862
-
Mm9::chr3:58999017..58999032,-p1@Gpr87
Mm9::chr3:90330747..90330754,+p2@S100a14
Mm9::chr3:90330778..90330781,+p3@S100a14
Mm9::chr3:90330783..90330803,+p1@S100a14
Mm9::chr3:90331064..90331098,+p@chr3:90331064..90331098
+
Mm9::chr3:90341164..90341192,+p5@S100a16
Mm9::chr5:93391094..93391119,+p12@Shroom3
Mm9::chrX:73088285..73088302,-p3@Pls3


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:0002065columnar/cuboidal epithelial cell differentiation0.0240456913519203
GO:0002066columnar/cuboidal epithelial cell development0.0240456913519203
GO:0005509calcium ion binding0.0240456913519203
GO:0003779actin binding0.0379414070840661
GO:0002064epithelial cell development0.0379414070840661



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
respiratory tract1.99e-0841
respiratory system4.80e-0842
thoracic cavity element1.80e-0717
thoracic segment organ1.80e-0717
thoracic cavity1.80e-0717
thoracic segment of trunk1.80e-0717
respiratory primordium1.80e-0717
endoderm of foregut1.80e-0717


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)
MA0003.10.0374387
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.11.56158
MA0017.10.207884
MA0019.11.39291
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
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
MA0048.10.769903
MA0050.10.365212
MA0051.11.18756
MA0052.10.76328
MA0055.10.136328
MA0056.10
MA0057.10.71676
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.12.04604
MA0063.10
MA0066.11.1475
MA0067.11.08124
MA0068.10.187364
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0103656
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.534411
MA0089.10
MA0090.12.24963
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.11.05226
MA0101.10.73212
MA0103.11.16365
MA0105.11.95127
MA0106.10.509454
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
MA0119.11.34784
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.11.11539
MA0139.10.103495
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.452699
MA0145.10.903527
MA0146.10.331601
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.20.412747
MA0039.20.675078
MA0138.20.555696
MA0002.20.343346
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.133279
MA0065.20.033123
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.434137
MA0155.10.637282
MA0156.11.851
MA0157.10.606944
MA0158.10
MA0159.10.957875
MA0160.10.347545
MA0161.10
MA0162.10.00661648
MA0163.10.0308606
MA0164.10.437937
MA0080.21.14688
MA0018.20.446948
MA0099.21.35508
MA0079.20.534138
MA0102.21.45844
MA0258.10.421574
MA0259.10.14914
MA0442.10
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