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MCL coexpression mm9:872: Difference between revisions

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{{MCL_coexpression_mm9
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geranylgeranyltransferase activity;0.0271713820930177;225467!GO:0004661;protein geranylgeranyltransferase 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!5.76e-11!25;UBERON:0002330!5.76e-11!25;UBERON:0005177!1.16e-10!79;UBERON:0002100!1.30e-09!90;UBERON:0001264!3.30e-09!12;UBERON:0002107!4.46e-09!22;UBERON:0007499!4.46e-09!22;UBERON:0006925!4.46e-09!22;UBERON:0009497!4.46e-09!22;UBERON:0000015!4.46e-09!22;UBERON:0002423!4.46e-09!22;UBERON:0006235!4.46e-09!22;UBERON:0008835!4.46e-09!22;UBERON:0003894!4.46e-09!22;UBERON:0004161!4.46e-09!22;UBERON:0008836!4.46e-09!22;UBERON:0009854!1.27e-08!23;UBERON:0009856!1.27e-08!23;UBERON:0004119!4.37e-08!118;UBERON:0000925!4.37e-08!118;UBERON:0006595!4.37e-08!118;UBERON:0005172!1.16e-07!49;UBERON:0005173!1.16e-07!49;UBERON:0002417!1.16e-07!49;UBERON:0000916!1.16e-07!49;UBERON:0000466!1.35e-07!79;UBERON:0000949!1.91e-07!72;UBERON:0001007!2.18e-07!116;UBERON:0001555!2.18e-07!116;UBERON:0007026!2.18e-07!116;UBERON:0005256!3.27e-07!45;UBERON:0003104!3.69e-07!61;UBERON:0009142!3.69e-07!61;UBERON:0004921!3.93e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,1.13872,0.538088,0.173246,1.02512,0.386846,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.938682,1.03863,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.153291,1.18318,0.303071,1.80488,0.455168,0.843667,0.699026,0.425071,0.757987,3.69395,0.242032,0.522578,0.221921,2.41256,0.256422,0.460258,0.204736,0.761266,0.403938,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.362495,0.985264,2.29155,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,1.49002,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,1.0125,0.50864,1.03623,0.433216,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,1.79411,0.612313,0.968721,0.920903,0.491838,1.68006,1.23935,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.585369,1.56229,1.99856,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.887702,0.386136,0.96962,0.337254,2.16002,1.21576,0.254749,0.143112,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,1.16726,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.203102,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,1.76938,0.714896,0.562634,0.676555,1.30183,0.0628627
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;1.10905,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.804572,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,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;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;1.2091,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;2.42557,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;0.214367,MA0074.1;0.531046,MA0076.1;0.845594,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;1.82974,MA0093.1;0.289361,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;1.85023,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;0.169849,MA0140.1;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;1.19766,MA0145.1;1.35361,MA0146.1;0.0771944,MA0147.1;1.24068,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,MA0035.2;0.524137,MA0039.2;0.402847,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.863775,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.902537,MA0150.1;1.07698,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.0804339,MA0156.1;0.314185,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;0.431684,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:75031386..75031390,+p12@Ggt1
Mm9::chr10:75031393..75031418,+p2@Ggt1
Mm9::chr11:5420954..5420969,+p2@Xbp1
Mm9::chr15:25870601..25870689,+p3@Fam134b
Mm9::chr15:98558537..98558548,-p2@Fkbp11
Mm9::chr15:98558551..98558618,-p1@Fkbp11
Mm9::chr6:28430337..28430370,+p2@Snd1
Mm9::chr6:28430386..28430413,+p1@Snd1


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:0004662CAAX-protein geranylgeranyltransferase activity0.0271713820930177
GO:0004661protein geranylgeranyltransferase activity0.0407436763680501



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
exocrine gland5.76e-1125
exocrine system5.76e-1125
trunk region element1.16e-1079
trunk1.30e-0990
pancreas3.30e-0912
liver4.46e-0922
epithelial sac4.46e-0922
digestive gland4.46e-0922
epithelium of foregut-midgut junction4.46e-0922
anatomical boundary4.46e-0922
hepatobiliary system4.46e-0922
foregut-midgut junction4.46e-0922
hepatic diverticulum4.46e-0922
liver primordium4.46e-0922
septum transversum4.46e-0922
liver bud4.46e-0922
digestive tract diverticulum1.27e-0823
sac1.27e-0823
endoderm-derived structure4.37e-08118
endoderm4.37e-08118
presumptive endoderm4.37e-08118
abdomen element1.16e-0749
abdominal segment element1.16e-0749
abdominal segment of trunk1.16e-0749
abdomen1.16e-0749
immaterial anatomical entity1.35e-0779
endocrine system1.91e-0772
digestive system2.18e-07116
digestive tract2.18e-07116
primitive gut2.18e-07116
trunk mesenchyme3.27e-0745
mesenchyme3.69e-0761
entire embryonic mesenchyme3.69e-0761
subdivision of digestive tract3.93e-07114


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)
MA0003.10.016751
MA0004.11.10905
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
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
MA0048.11.13456
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.12.42557
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
MA0073.10.214367
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.11.82974
MA0093.10.289361
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
MA0114.11.85023
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
MA0139.10.169849
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.11.19766
MA0145.11.35361
MA0146.10.0771944
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.20.402847
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.20.902537
MA0150.11.07698
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
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
MA0079.20.431684
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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