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MCL coexpression mm9:350: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!4.02e-10!333;UBERON:0002048!1.34e-07!14;UBERON:0000117!1.34e-07!14;UBERON:0000171!1.34e-07!14;UBERON:0000170!1.34e-07!14;UBERON:0005597!1.34e-07!14;UBERON:0000118!1.34e-07!14;UBERON:0005153!1.82e-07!17;UBERON:0000464!6.66e-07!57
|ontology_enrichment_uberon=UBERON:0000468!4.02e-10!333;UBERON:0002048!1.34e-07!14;UBERON:0000117!1.34e-07!14;UBERON:0000171!1.34e-07!14;UBERON:0000170!1.34e-07!14;UBERON:0005597!1.34e-07!14;UBERON:0000118!1.34e-07!14;UBERON:0005153!1.82e-07!17;UBERON:0000464!6.66e-07!57
|tfbs_overrepresentation_for_novel_motifs=0.119369,0.649613,0.341317,2.71559,0.425918,0.15366,0.214952,0.711075,0.752205,0.11695,0.184424,0.206436,1.8816,0.223743,0.211839,0,0.977447,0.0483719,0.393073,1.68478,0.0854539,0.495413,0.63467,0.189689,0.108863,0.243873,0.369214,0.167184,0.53096,0.443023,0.477864,0.460285,0.0475156,0.315369,1.22632,0.00780406,0.0440547,0.2039,2.35262,0.277918,0.416906,0.161379,1.144,0.0590946,0.0608974,0.426921,0.309657,0.177618,1.21544,0.252327,0.359925,0.264025,0.113338,0.586014,0.601849,0.22892,0.559359,0.197526,0.173818,0.227439,0.442975,0.746278,0.269556,0.350689,0.237053,0.384144,0.727642,1.06142,0.438956,0.919268,0.314287,1.08045,0.20691,0.632466,0.0612875,0.0536469,0.157028,0.300684,1.92081,0.295115,0.45844,0.388829,0.743757,0.683588,0.5282,0.00146799,0.0633883,0.122924,0.313544,1.21975,0.793151,0.532634,0.471416,0.198642,0.0351424,3.27942,0.429553,0.473864,0.309859,0.00586625,0.0440835,1.16381,0.570262,0.360414,0.359547,0.161095,0.409409,0.174935,0.301886,0.0863521,0.369309,0.57187,0.296684,0.187937,0.799811,0.184628,0.574792,1.41908,0.375433,0.0427125,0.637418,0.333667,0.245224,0.299972,0.851175,0.43141,0.220786,0.465518,0.726225,0.777839,0.554981,0.432886,0.698665,1.2483,0.820264,0.0109134,0.124253,0.162291,0.773792,1.58317,1.18855,0.732048,2.01648,0.469382,0.35423,0.486829,0.31213,1.54387,0.790363,0.0521541,0.261373,0.00126457,0.587436,0.30395,0.238221,0.662158,1.34508,0.226926,0.117954,0.124089,0.782756,0.527439,0.431791,0.738623,0.351524,0.657421,1.0487,0.205322,0.0723599
|tfbs_overrepresentation_for_novel_motifs=0.119369,0.649613,0.341317,2.71559,0.425918,0.15366,0.214952,0.711075,0.752205,0.11695,0.184424,0.206436,1.8816,0.223743,0.211839,0,0.977447,0.0483719,0.393073,1.68478,0.0854539,0.495413,0.63467,0.189689,0.108863,0.243873,0.369214,0.167184,0.53096,0.443023,0.477864,0.460285,0.0475156,0.315369,1.22632,0.00780406,0.0440547,0.2039,2.35262,0.277918,0.416906,0.161379,1.144,0.0590946,0.0608974,0.426921,0.309657,0.177618,1.21544,0.252327,0.359925,0.264025,0.113338,0.586014,0.601849,0.22892,0.559359,0.197526,0.173818,0.227439,0.442975,0.746278,0.269556,0.350689,0.237053,0.384144,0.727642,1.06142,0.438956,0.919268,0.314287,1.08045,0.20691,0.632466,0.0612875,0.0536469,0.157028,0.300684,1.92081,0.295115,0.45844,0.388829,0.743757,0.683588,0.5282,0.00146799,0.0633883,0.122924,0.313544,1.21975,0.793151,0.532634,0.471416,0.198642,0.0351424,3.27942,0.429553,0.473864,0.309859,0.00586625,0.0440835,1.16381,0.570262,0.360414,0.359547,0.161095,0.409409,0.174935,0.301886,0.0863521,0.369309,0.57187,0.296684,0.187937,0.799811,0.184628,0.574792,1.41908,0.375433,0.0427125,0.637418,0.333667,0.245224,0.299972,0.851175,0.43141,0.220786,0.465518,0.726225,0.777839,0.554981,0.432886,0.698665,1.2483,0.820264,0.0109134,0.124253,0.162291,0.773792,1.58317,1.18855,0.732048,2.01648,0.469382,0.35423,0.486829,0.31213,1.54387,0.790363,0.0521541,0.261373,0.00126457,0.587436,0.30395,0.238221,0.662158,1.34508,0.226926,0.117954,0.124089,0.782756,0.527439,0.431791,0.738623,0.351524,0.657421,1.0487,0.205322,0.0723599
|tfbs_overrepresentation_jaspar=MA0003.1;0.132368,MA0004.1;0.144883,MA0006.1;0.2064,MA0007.1;0.421767,MA0009.1;0.483331,MA0014.1;0.00543855,MA0017.1;0.239891,MA0019.1;0.878507,MA0024.1;0.445298,MA0025.1;0.694475,MA0027.1;2.07936,MA0028.1;0.0607913,MA0029.1;0.426655,MA0030.1;1.10385,MA0031.1;0.402033,MA0038.1;0.243815,MA0040.1;1.23731,MA0041.1;1.12403,MA0042.1;1.07583,MA0043.1;0.569356,MA0046.1;0.514989,MA0048.1;1.89609,MA0050.1;0.169675,MA0051.1;0.250459,MA0052.1;1.25247,MA0055.1;2.65356,MA0056.1;0,MA0057.1;0.0819723,MA0058.1;0.0904678,MA0059.1;0.0968666,MA0060.1;0.0282014,MA0061.1;0.343057,MA0063.1;0,MA0066.1;0.664275,MA0067.1;0.798606,MA0068.1;0.341633,MA0069.1;0.501715,MA0070.1;0.493176,MA0071.1;0.974672,MA0072.1;0.485733,MA0073.1;4.72572e-07,MA0074.1;0.209912,MA0076.1;0.0767377,MA0077.1;4.12597,MA0078.1;0.275441,MA0081.1;1.18104,MA0083.1;0.568641,MA0084.1;1.11388,MA0087.1;1.31333,MA0088.1;0.333856,MA0089.1;0,MA0090.1;0.392445,MA0091.1;2.0912,MA0092.1;0.124428,MA0093.1;0.0643828,MA0095.1;0,MA0098.1;0,MA0100.1;1.10548,MA0101.1;0.681587,MA0103.1;0.54098,MA0105.1;0.515449,MA0106.1;0.281418,MA0107.1;0.526347,MA0108.2;0.348212,MA0109.1;0,MA0111.1;0.413949,MA0113.1;0.720329,MA0114.1;0.338149,MA0115.1;0.571881,MA0116.1;0.206147,MA0117.1;0.542889,MA0119.1;0.101951,MA0122.1;0.560692,MA0124.1;0.748494,MA0125.1;0.67944,MA0130.1;0,MA0131.1;0.326061,MA0132.1;0,MA0133.1;0,MA0135.1;0.602346,MA0136.1;0.637057,MA0139.1;0.0885364,MA0140.1;1.73546,MA0141.1;0.0822433,MA0142.1;0.389844,MA0143.1;0.27232,MA0144.1;0.971501,MA0145.1;0.115721,MA0146.1;0.709805,MA0147.1;0.0420513,MA0148.1;0.470482,MA0149.1;2.96597,MA0062.2;0.0591193,MA0035.2;1.11804,MA0039.2;0.312857,MA0138.2;0.319705,MA0002.2;0.706893,MA0137.2;0.080825,MA0104.2;0.0242964,MA0047.2;0.243248,MA0112.2;0.0488517,MA0065.2;0.223525,MA0150.1;0.135628,MA0151.1;0,MA0152.1;0.243327,MA0153.1;0.617506,MA0154.1;0.360977,MA0155.1;0.438423,MA0156.1;3.21167,MA0157.1;0.363212,MA0158.1;0,MA0159.1;0.174007,MA0160.1;0.156994,MA0161.1;0,MA0162.1;0.0144065,MA0163.1;0.00340854,MA0164.1;0.224368,MA0080.2;3.10102,MA0018.2;0.231394,MA0099.2;0.314682,MA0079.2;0.00220522,MA0102.2;1.16504,MA0258.1;0.131525,MA0259.1;0.0383313,MA0442.1;0
}}
}}

Revision as of 11:36, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:101755013..101755094,-p@chr11:101755013..101755094
-
Mm9::chr11:30143050..30143055,-p@chr11:30143050..30143055
-
Mm9::chr17:10423983..10423987,-p@chr17:10423983..10423987
-
Mm9::chr17:24781878..24781921,-p2@Slc9a3r2
Mm9::chr2:179997285..179997300,-p@chr2:179997285..179997300
-
Mm9::chr5:136019136..136019144,-p@chr5:136019136..136019144
-
Mm9::chr6:91671712..91671734,+p@chr6:91671712..91671734
+
Mm9::chr7:80885163..80885219,+p2@Fam174b
Mm9::chr8:12926192..12926201,+p14@Mcf2l
Mm9::chr8:12926204..12926218,+p11@Mcf2l
Mm9::chr8:12926268..12926291,+p2@Mcf2l
Mm9::chr8:12926299..12926317,+p4@Mcf2l
Mm9::chr9:48122532..48122588,+p@chr9:48122532..48122588
+
Mm9::chr9:60713920..60713971,+p@chr9:60713920..60713971
+
Mm9::chr9:79809768..79809783,-p11@Filip1
Mm9::chr9:79809790..79809808,-p7@Filip1
Mm9::chrX:18038392..18038406,-p3@4930578C19Rik
Mm9::chrX:18038411..18038449,-p1@4930578C19Rik
Mm9::chrX:18038511..18038528,-p2@4930578C19Rik
Mm9::chrX:6154428..6154445,+p6@Shroom4
Mm9::chrX:7258341..7258355,-p3@Magix
Mm9::chrX:7258356..7258382,-p2@Magix


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:0016324apical plasma membrane0.0123051114716402
GO:0045177apical part of cell0.0152455547678518
GO:0001757somite specification0.0384173101686729
GO:0009898internal side of plasma membrane0.0384173101686729
GO:0005545phosphatidylinositol binding0.0384173101686729
GO:0031941filamentous actin0.0384173101686729
GO:0007379segment specification0.0384173101686729
GO:0009925basal plasma membrane0.0384173101686729
GO:0045178basal part of cell0.0384173101686729
GO:0030864cortical actin cytoskeleton0.0422474663285222



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
multi-cellular organism4.02e-10333
lung1.34e-0714
respiratory tube1.34e-0714
respiration organ1.34e-0714
pair of lungs1.34e-0714
lung primordium1.34e-0714
lung bud1.34e-0714
epithelial bud1.82e-0717
anatomical space6.66e-0757


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)
MA0003.10.132368
MA0004.10.144883
MA0006.10.2064
MA0007.10.421767
MA0009.10.483331
MA0014.10.00543855
MA0017.10.239891
MA0019.10.878507
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.0607913
MA0029.10.426655
MA0030.11.10385
MA0031.10.402033
MA0038.10.243815
MA0040.11.23731
MA0041.11.12403
MA0042.11.07583
MA0043.10.569356
MA0046.10.514989
MA0048.11.89609
MA0050.10.169675
MA0051.10.250459
MA0052.11.25247
MA0055.12.65356
MA0056.10
MA0057.10.0819723
MA0058.10.0904678
MA0059.10.0968666
MA0060.10.0282014
MA0061.10.343057
MA0063.10
MA0066.10.664275
MA0067.10.798606
MA0068.10.341633
MA0069.10.501715
MA0070.10.493176
MA0071.10.974672
MA0072.10.485733
MA0073.14.72572e-07
MA0074.10.209912
MA0076.10.0767377
MA0077.14.12597
MA0078.10.275441
MA0081.11.18104
MA0083.10.568641
MA0084.11.11388
MA0087.11.31333
MA0088.10.333856
MA0089.10
MA0090.10.392445
MA0091.12.0912
MA0092.10.124428
MA0093.10.0643828
MA0095.10
MA0098.10
MA0100.11.10548
MA0101.10.681587
MA0103.10.54098
MA0105.10.515449
MA0106.10.281418
MA0107.10.526347
MA0108.20.348212
MA0109.10
MA0111.10.413949
MA0113.10.720329
MA0114.10.338149
MA0115.10.571881
MA0116.10.206147
MA0117.10.542889
MA0119.10.101951
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.10.0885364
MA0140.11.73546
MA0141.10.0822433
MA0142.10.389844
MA0143.10.27232
MA0144.10.971501
MA0145.10.115721
MA0146.10.709805
MA0147.10.0420513
MA0148.10.470482
MA0149.12.96597
MA0062.20.0591193
MA0035.21.11804
MA0039.20.312857
MA0138.20.319705
MA0002.20.706893
MA0137.20.080825
MA0104.20.0242964
MA0047.20.243248
MA0112.20.0488517
MA0065.20.223525
MA0150.10.135628
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.360977
MA0155.10.438423
MA0156.13.21167
MA0157.10.363212
MA0158.10
MA0159.10.174007
MA0160.10.156994
MA0161.10
MA0162.10.0144065
MA0163.10.00340854
MA0164.10.224368
MA0080.23.10102
MA0018.20.231394
MA0099.20.314682
MA0079.20.00220522
MA0102.21.16504
MA0258.10.131525
MA0259.10.0383313
MA0442.10
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