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MCL coexpression mm9:436: Difference between revisions

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{{MCL_coexpression_mm9
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to membrane;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0031224;intrinsic to membrane;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0005046;KDEL sequence binding;0.04809804862303;68137!GO:0044425;membrane part;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0046923;ER retention sequence binding;0.04809804862303;68137!GO:0006621;protein retention in ER;0.04809804862303;68137!GO:0016192;vesicle-mediated transport;0.04809804862303;68090,68137,65107!GO:0016020;membrane;0.04809804862303;17000,66220,18220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0043120;tumor necrosis factor binding;0.04809804862303;21937!GO:0005031;tumor necrosis factor receptor 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|gostat_on_MCL_coexpression=GO:0016021;integral to membrane;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0031224;intrinsic to membrane;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0005046;KDEL sequence binding;0.04809804862303;68137!GO:0044425;membrane part;0.04809804862303;17000,66220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0046923;ER retention sequence binding;0.04809804862303;68137!GO:0006621;protein retention in ER;0.04809804862303;68137!GO:0016192;vesicle-mediated transport;0.04809804862303;68090,68137,65107!GO:0016020;membrane;0.04809804862303;17000,66220,18220,28064,68137,21937,65107,74140,20598,68090,226548!GO:0043120;tumor necrosis factor binding;0.04809804862303;21937!GO:0005031;tumor necrosis factor receptor activity;0.04809804862303;21937!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.18e-10!31;UBERON:0002100!6.96e-09!90;UBERON:0005409!6.50e-08!47;UBERON:0005256!7.51e-08!45;UBERON:0003104!2.42e-07!61;UBERON:0009142!2.42e-07!61
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.640544,0.476315,0.593409,0.0882392,0.216369,0.782043,0.165361,0.705534,0.427945,0.702345,0.760086,0.376789,0.804507,0.0975425,0,0.46143,0.285124,1.37851,0.53564,0.823639,0.585659,1.45942,0.294623,0.489022,0.85524,0.322606,0.232181,1.21407,1.05093,0.22152,0.552579,0.281806,0.116244,0.322914,0.144175,0.566587,0.753507,0.510225,0.43804,0.290922,0.640129,0.00488374,0.325245,2.00542,0.197508,0.391673,0.244272,0.018895,0.748156,1.13348,0.341665,0.416592,0.683824,0.700221,0.817643,0.121631,0.26711,0.302464,0.300938,0.534331,0.922742,0.427506,0.43605,1.51574,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.0453143,0.22592,0.731855,0.846083,0.493181,0.518029,0.381898,0.518764,0.835355,0.0458011,0.476893,0.348372,0.64715,0.623727,0.390032,0.0332815,0.715057,0.395899,1.32869,0.896685,0.62835,0.564287,0.0914951,0.499944,0.207461,0.162339,0.56686,1.01594,0.369986,0.0779031,0.552324,0.667487,1.98244,0.445567,0.225081,1.24688,0.241171,0.43037,0.418437,0.170493,0.669156,0.838495,0.711663,0.903482,0.288262,0.205053,0.208431,0.462587,0.262826,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,1.37283,0.828246,1.07003,0.651613,0.580662,0.799981,0.313768,0.92434,0.204108,0.534959,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,1.38142,0.439856,0.225756,0.394362,1.65442,0.183006,0.0892035,0.447655,0.327556,0.685297,0.0594762,0.841089,0.762455,0.342508,0.340691,0.173692,2.30461,0.886073,0.622933,0.522515,0.50469,0.436947,0.306938,0.266569,0.275979,3.54639
}}

Latest revision as of 15:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:41210141..41210174,-p1@Smpd2
Mm9::chr14:55082978..55083059,+p1@Lrp10
Mm9::chr14:56262143..56262219,-p1@Tm9sf1
Mm9::chr17:46385018..46385088,+p1@Yipf3
Mm9::chr17:56429922..56429952,-p1@Plin3
Mm9::chr19:4148684..4148697,+p2@Coro1b
Mm9::chr19:5088534..5088575,+p1@Yif1a
Mm9::chr19:5088580..5088591,+p2@Yif1a
Mm9::chr2:29949162..29949199,-p3@Zdhhc12
Mm9::chr3:95697876..95697897,+p1@Aph1a
Mm9::chr6:124758916..124758951,+p1@Spsb2
Mm9::chr6:125263843..125263854,-p3@Ltbr
Mm9::chr6:125263862..125263896,-p1@Ltbr
Mm9::chr6:125299717..125299793,+p1@Tnfrsf1a
Mm9::chr7:52765736..52765769,-p1@Nucb1
Mm9::chr7:53128171..53128227,+p1@Kdelr1
Mm9::chr7:53128232..53128252,+p2@Kdelr1


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:0016021integral to membrane0.04809804862303
GO:0031224intrinsic to membrane0.04809804862303
GO:0005046KDEL sequence binding0.04809804862303
GO:0044425membrane part0.04809804862303
GO:0046923ER retention sequence binding0.04809804862303
GO:0006621protein retention in ER0.04809804862303
GO:0016192vesicle-mediated transport0.04809804862303
GO:0016020membrane0.04809804862303
GO:0043120tumor necrosis factor binding0.04809804862303
GO:0005031tumor necrosis factor receptor activity0.04809804862303



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
intestine1.18e-1031
trunk6.96e-0990
gastrointestinal system6.50e-0847
trunk mesenchyme7.51e-0845
mesenchyme2.42e-0761
entire embryonic mesenchyme2.42e-0761


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)
MA0003.12.74535
MA0004.10.594255
MA0006.10.650564
MA0007.10.56814
MA0009.10.576798
MA0014.11.35861
MA0017.11.18801
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.11.65334
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.855094
MA0040.10.588314
MA0041.10.152751
MA0042.10.144042
MA0043.10.666547
MA0046.10.609938
MA0048.10.619737
MA0050.10.235075
MA0051.10.326637
MA0052.10.595747
MA0055.10.0306466
MA0056.10
MA0057.10.56493
MA0058.10.851133
MA0059.10.451977
MA0060.11.65623
MA0061.10.0684878
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.176958
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.16.24648e-05
MA0074.10.281183
MA0076.10.774399
MA0077.10.559443
MA0078.10.354249
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.11.18662
MA0089.10
MA0090.10.534933
MA0091.10.215731
MA0092.10.535473
MA0093.10.700866
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.153616
MA0103.10.373479
MA0105.10.111401
MA0106.10.360817
MA0107.10.113208
MA0108.20.433384
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.11.83838
MA0115.10.669167
MA0116.10.315135
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.11.85698
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.805431
MA0139.11.44988
MA0140.10.271883
MA0141.11.30903
MA0142.10.477975
MA0143.10.350815
MA0144.10.242681
MA0145.10.654323
MA0146.13.05873
MA0147.10.260161
MA0148.10.218033
MA0149.10.157322
MA0062.22.64517
MA0035.21.38497
MA0039.22.20258
MA0138.20.402586
MA0002.20.0425713
MA0137.20.127311
MA0104.20.720139
MA0047.20.318614
MA0112.25.2531
MA0065.22.51795
MA0150.10.195003
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.11.67224
MA0155.10.484511
MA0156.11.26033
MA0157.10.4495
MA0158.10
MA0159.10.578474
MA0160.10.220282
MA0161.10
MA0162.11.1829
MA0163.11.37382
MA0164.10.297489
MA0080.20.737223
MA0018.21.49302
MA0099.20.397135
MA0079.24.41442
MA0102.21.27355
MA0258.12.3051
MA0259.10.896382
MA0442.10
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