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<h1 class="title toc-ignore">Enrichment results of fasting glucose</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
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<p><strong>Last updated:</strong> 2018-10-05</p>
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<div id="input-data" class="section level2">
<h2>Input data</h2>
<p>Results below were generated from the GWAS summary statistics published in the paper <a href="https://www.ncbi.nlm.nih.gov/pubmed/22581228">“A Genome-Wide Approach Accounting for Body Mass Index Identifies Genetic Variants Influencing Fasting Glycemic Traits and Insulin Resistance” (<em>Nature Genetics</em>, 2012)</a>. The summary data file is available at <a href="http://www.magicinvestigators.org/downloads" class="uri">http://www.magicinvestigators.org/downloads</a>.</p>
</div>
<div id="analysis-results" class="section level2">
<h2>Analysis results</h2>
<p>Enrichment analyses are summarized by the following three quantities.</p>
<ul>
<li><strong>BF:</strong> Bayes factor comparing the enrichment model against the baseline model;</li>
<li><strong>Outside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “outside” the gene set;</li>
<li><strong>Inside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “inside” the gene set.</li>
</ul>
<p>The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.</p>
<div id="biological-pathways" class="section level3">
<h3>Biological pathways</h3>
<div id="htmlwidget-983860bb2d7d6ad3a872" style="width:100%;height:auto;" class="datatables html-widget"></div>
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GTPases<br/>(reactome, BioSystems)","Synthesis of bile acids and bile salts<br/>(reactome, PC)","Nuclear Receptors in Lipid Metabolism and Toxicity<br/>(biocarta, BioCarta)","Bile secretion<br/>(kegg, BioSystems)","Nuclear receptors in lipid metabolism and toxicity<br/>(wiki, BioSystems)","Carbohydrate metabolism<br/>(reactome, PC)","Metabolism of carbohydrates<br/>(reactome, BioSystems)","Starch and sucrose...<br/>(kegg, PC)","Insulin signaling pathway<br/>(kegg, BioSystems)","gluconeogenesis<br/>(humancyc, PC)","Glycolysis / Gluconeogenesis<br/>(kegg, BioSystems)","Adipocytokine signaling pathway<br/>(kegg, BioSystems)","Cell Cycle, Mitotic<br/>(reactome, BioSystems)","FoxO signaling pathway<br/>(kegg, BioSystems)","PI3K-Akt signaling pathway<br/>(kegg, BioSystems)","AMPK signaling pathway<br/>(kegg, BioSystems)","Insulin secretion<br/>(kegg, BioSystems)","Regulation of beta-cell development<br/>(reactome, PC)","Maturity onset diabetes of the young<br/>(kegg, BioSystems)","Regulation of gene expression in beta cells<br/>(reactome, PC)","Central carbon metabolism in cancer<br/>(kegg, BioSystems)","Activation of cAMP-dependent protein kinase, PKA<br/>(biocarta, BioCarta)","Mitotic Metaphase and Anaphase<br/>(reactome, BioSystems)","Lactose synthesis<br/>(reactome, BioSystems)","Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells<br/>(reactome, PC)","Regulation of Glucokinase by Glucokinase Regulatory Protein<br/>(reactome, BioSystems)","RHO GTPase Effectors<br/>(reactome, BioSystems)","Facilitative Na+-independent glucose transporters<br/>(reactome, BioSystems)","Mitotic M-M/G1 phases<br/>(reactome, PC)","Glucagon signaling pathway<br/>(kegg, BioSystems)","Cell Cycle, Mitotic<br/>(reactome, PC)","Validated targets of C-MYC transcriptional activation<br/>(pid, PC)","Validated targets of C-MYC transcriptional activation<br/>(pid, BioSystems)","Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds<br/>(reactome, BioSystems)","Glycolysis and Gluconeogenesis<br/>(wiki, BioSystems)","Regulation of Glucokinase by Glucokinase Regulatory Protein<br/>(reactome, PC)","HIF-1 signaling pathway<br/>(kegg, BioSystems)","Regulation of insulin secretion<br/>(reactome, BioSystems)","Integration of energy metabolism<br/>(reactome, BioSystems)","Integration of energy metabolism<br/>(reactome, PC)","Regulation of insulin secretion<br/>(reactome, PC)","HIF-1-alpha transcription factor network<br/>(pid, PC)","IL-3 Signaling Pathway<br/>(wiki, BioSystems)","HIF-1-alpha transcription factor network<br/>(pid, BioSystems)","cAMP signaling<br/>(kegg, BioSystems)","Transcriptional misregulation in cancer<br/>(kegg, BioSystems)","Defective AMN causes hereditary megaloblastic anemia 1<br/>(reactome, PC)","Metabolism of water-soluble vitamins and cofactors<br/>(reactome, BioSystems)","Vitamin C in the Brain<br/>(biocarta, BioCarta)","HIF-2-alpha transcription factor network<br/>(pid, PC)","Regulation of Commissural axon pathfinding by Slit and Robo<br/>(reactome, PC)","b-arrestins in GPCR Desensitization<br/>(biocarta, BioCarta)","Renal cell carcinoma<br/>(kegg, BioSystems)","Vitamin C (ascorbate) metabolism<br/>(reactome, PC)","Signaling by Robo receptor<br/>(reactome, PC)","Phospholipase C-epsilon pathway<br/>(biocarta, BioCarta)","Ion Channels and Their Functional Role in Vascular Endothelium<br/>(biocarta, BioCarta)","Estrogen signaling pathway<br/>(wiki, BioSystems)","Prostacyclin signalling through prostacyclin receptor<br/>(reactome, PC)","Retrograde neurotrophin signalling<br/>(reactome, PC)","Corticosteroids and cardioprotection<br/>(biocarta, BioCarta)","Serotonin Receptor 4/6/7 and NR3C Signaling<br/>(wiki, BioSystems)","Attenuation of GPCR Signaling<br/>(biocarta, BioCarta)","Thyroid hormone signaling pathway<br/>(kegg, BioSystems)"],[47,39,44,14,254,288,29,20,94,17,163,45,5,16,104,42,26,9,164,35,19,15,6,153,156,15,102,56,24,36,41,96,112,166,251,284,375,27,14,70,33,244,253,23,133,23,64,67,463,128,335,120,82,32,25,20,64,6,167,3,5,29,274,13,316,96,457,78,79,98,47,28,98,78,104,101,75,65,98,64,13,170,86,86,9,32,4,10,64,8,31,12,7,19,19,13,19,18,13,114],[4033,3322,3934,1021,26227,20388,2847,1794,8334,2294,13285,3859,503,1905,9073,4691,2473,998,13416,3797,1713,1832,861,12324,12440,1683,8962,3985,2457,3870,3496,8445,10004,13401,25704,20175,34974,2835,1484,8023,3724,24717,25354,2684,12126,1713,5046,6918,34662,12136,35192,12916,12527,2956,2278,1724,6151,490,13532,346,418,2451,20760,1193,22765,10393,34253,6253,6253,9797,3873,2354,10543,10257,12883,12653,10027,7131,9587,6506,1818,16048,8777,8777,1065,2989,1503,1402,6362,684,4769,1163,1345,2023,1598,1626,1892,1823,1734,12369],[1898.39083384662,1655.18379472399,1540.01503745955,1511.19946193481,1444.67799330816,1400.87498216408,1396.54910219854,1372.29445718131,1371.72974109376,1338.76069704217,1333.45466634146,1324.19084230479,1310.58863606851,1295.33765231045,1293.8413055239,1290.33082013672,1287.70780216713,1276.43928203042,1276.23529976706,1259.87052607588,1259.23019017105,1253.14144675827,1247.43395226777,1233.6461641202,1223.77768799332,1222.82965380509,1217.6698061286,1213.91358199707,1203.67220066754,1199.11815189623,1197.24863576734,1197.10861465916,1196.22818032197,1195.51415116307,1194.37354806137,1184.44893247864,1184.38708173217,1180.799321616,1151.60520111785,1150.63298101694,1149.07435319818,1131.72414633205,1103.35842311701,1101.00831618508,1094.94678939157,1087.60101938337,1086.6100754179,1072.47343064008,1066.72338611556,1059.25738927235,1047.49828623833,1041.3196773055,880.517365084793,873.102583383589,828.115908370933,814.052172064865,811.36831544089,778.857735741777,696.488580563228,656.702737437502,240.314265926875,209.565248929021,168.571794628904,116.873874327217,69.2532521977831,41.9183852620325,27.802980349427,10.0304984968716,10.0304984968716,7.82053476812335,4.29657227538804,3.51614703332535,3.45277465751258,2.32538992786112,2.17844279358362,2.17075915833305,2.14458414041147,1.76652522437379,1.29158714062274,1.12430093129235,0.648260906812578,0.331925737724022,0.120090771929083,0.120090771929083,-0.00293232146797972,-0.00341496651650491,-0.00408132368656688,-0.00779629763315869,-0.013004783191034,-0.0174357580856289,-0.0187676364720273,-0.0245175386905544,-0.0245390119196935,-0.0384592316372087,-0.0406112817074944,-0.047869509060749,-0.0609335582773727,-0.0784762772504652,-0.135210087108475,-0.16863112828997],["-4.8048<br/>[-4.8048, -4.8048]","-4.8051<br/>[-4.8051, -4.8051]","-4.6952<br/>[-4.6952, -4.6952]","-4.6778<br/>[-4.6778, -4.6778]","-4.8491<br/>[-4.8491, -4.8491]","-4.6702<br/>[-4.6702, -4.6702]","-4.7159<br/>[-4.7159, -4.7159]","-4.6966<br/>[-4.6966, -4.6966]","-4.6750<br/>[-4.6750, -4.6750]","-4.6589<br/>[-4.6589, -4.6589]","-4.6730<br/>[-4.6730, -4.6730]","-4.8049<br/>[-4.8049, -4.8049]","-4.6971<br/>[-4.6971, -4.6971]","-4.6591<br/>[-4.6591, -4.6591]","-4.6747<br/>[-4.6747, -4.6747]","-4.6580<br/>[-4.6580, -4.6580]","-4.7160<br/>[-4.7160, -4.7160]","-4.6778<br/>[-4.6778, -4.6778]","-4.6730<br/>[-4.6730, -4.6730]","-4.6583<br/>[-4.6583, -4.6583]","-4.6966<br/>[-4.6966, -4.6966]","-4.6591<br/>[-4.6591, -4.6591]","-4.6595<br/>[-4.6595, -4.6595]","-4.6734<br/>[-4.6734, -4.6734]","-4.6734<br/>[-4.6734, -4.6734]","-4.7163<br/>[-4.7163, -4.7163]","-4.6747<br/>[-4.6747, -4.6747]","-4.7154<br/>[-4.7154, -4.7154]","-4.6589<br/>[-4.6589, -4.6589]","-4.6583<br/>[-4.6583, -4.6583]","-4.8050<br/>[-4.8050, -4.8050]","-4.6749<br/>[-4.6749, -4.6749]","-4.6743<br/>[-4.6743, -4.6743]","-4.6730<br/>[-4.6730, -4.6730]","-4.8493<br/>[-4.8493, -4.8493]","-4.6703<br/>[-4.6703, -4.6703]","-4.6654<br/>[-4.6654, -4.6654]","-4.6587<br/>[-4.6587, -4.6587]","-4.6745<br/>[-4.6745, -4.6745]","-4.6574<br/>[-4.6574, -4.6574]","-4.6736<br/>[-4.6736, -4.6736]","-4.7967<br/>[-4.7967, -4.7967]","-4.7964<br/>[-4.7964, -4.7964]","-4.7159<br/>[-4.7159, -4.7159]","-4.7123<br/>[-4.7123, -4.7123]","-4.6775<br/>[-4.6775, -4.6775]","-4.7150<br/>[-4.7150, -4.7150]","-4.6755<br/>[-4.6755, -4.6755]","-4.7197<br/>[-4.7197, -4.7197]","-4.6734<br/>[-4.6734, -4.6734]","-4.6643<br/>[-4.6643, -4.6643]","-4.6731<br/>[-4.6731, -4.6731]","-4.4478<br/>[-4.4478, -4.4478]","-4.4569<br/>[-4.4569, -4.4569]","-4.4572<br/>[-4.4572, -4.4572]","-4.4574<br/>[-4.4574, -4.4574]","-4.4498<br/>[-4.4498, -4.4498]","-4.4195<br/>[-4.4195, -4.4195]","-4.6729<br/>[-4.6729, -4.6729]","-4.4195<br/>[-4.4195, -4.4195]","-4.4195<br/>[-4.4195, -4.4195]","-4.4732<br/>[-4.4732, -4.4732]","-4.6701<br/>[-4.6701, -4.6701]","-4.4293<br/>[-4.4293, -4.4293]","-4.6693<br/>[-4.6693, -4.6693]","-4.7333<br/>[-4.7333, -4.7333]","-4.7199<br/>[-4.7199, -4.7199]","-4.4276<br/>[-4.4276, -4.4276]","-4.4276<br/>[-4.4276, -4.4276]","-4.4366<br/>[-4.4366, -4.4366]","-4.4498<br/>[-4.4498, -4.4498]","-4.4732<br/>[-4.4732, -4.4732]","-4.4365<br/>[-4.4365, -4.4365]","-4.4262<br/>[-4.4262, -4.4262]","-4.4252<br/>[-4.4252, -4.4252]","-4.4253<br/>[-4.4253, -4.4253]","-4.4263<br/>[-4.4263, -4.4263]","-4.4379<br/>[-4.4379, -4.4379]","-4.4246<br/>[-4.4246, -4.4246]","-4.4381<br/>[-4.4381, -4.4381]","-4.4194<br/>[-4.4194, -4.4194]","-4.4230<br/>[-4.4230, -4.4230]","-4.4162<br/>[-4.4162, -4.4162]","-4.4162<br/>[-4.4162, -4.4162]","-4.4193<br/>[-4.4193, -4.4193]","-4.4185<br/>[-4.4185, -4.4185]","-4.4191<br/>[-4.4191, -4.4191]","-4.4191<br/>[-4.4191, -4.4191]","-4.4172<br/>[-4.4172, -4.4172]","-4.4194<br/>[-4.4194, -4.4194]","-4.4178<br/>[-4.4178, -4.4178]","-4.4192<br/>[-4.4192, -4.4192]","-4.4191<br/>[-4.4191, -4.4191]","-4.4189<br/>[-4.4189, -4.4189]","-4.4190<br/>[-4.4190, -4.4190]","-4.4190<br/>[-4.4190, -4.4190]","-4.4189<br/>[-4.4189, -4.4189]","-4.4190<br/>[-4.4190, -4.4190]","-4.4190<br/>[-4.4190, -4.4190]","-4.4148<br/>[-4.4148, -4.4148]"],["-2.0140<br/>[-2.0140, -2.0042]","-1.9178<br/>[-1.9178, -1.9172]","-2.1800<br/>[-2.1800, -2.1800]","-1.5178<br/>[-1.5178, -1.5178]","-2.9420<br/>[-2.9420, -2.9420]","-2.9070<br/>[-2.9070, -2.9070]","-1.9572<br/>[-1.9573, -1.9561]","-1.8370<br/>[-1.8370, -1.8345]","-2.5056<br/>[-2.5056, -2.5056]","-1.9065<br/>[-1.9065, -1.9065]","-2.7759<br/>[-2.7930, -2.7759]","-2.1072<br/>[-2.1072, -2.1072]","-1.3566<br/>[-1.3566, -1.3566]","-1.9019<br/>[-1.9019, -1.9019]","-2.5979<br/>[-2.5979, -2.5979]","-2.2926<br/>[-2.2929, -2.2926]","-1.9618<br/>[-1.9618, -1.9618]","-1.5699<br/>[-1.5699, -1.5699]","-2.7773<br/>[-2.7773, -2.7773]","-2.1932<br/>[-2.1932, -2.1932]","-1.8017<br/>[-1.8017, -1.8017]","-1.9037<br/>[-1.9037, -1.9037]","-1.5563<br/>[-1.5563, -1.5563]","-2.7611<br/>[-2.7611, -2.7611]","-2.7662<br/>[-2.7662, -2.7662]","-1.7851<br/>[-1.7851, -1.7851]","-2.6289<br/>[-2.6289, -2.6289]","-2.1757<br/>[-2.1757, -2.1757]","-2.0478<br/>[-2.0478, -2.0478]","-2.2258<br/>[-2.2258, -2.2258]","-2.0778<br/>[-2.0778, -2.0778]","-2.6029<br/>[-2.6031, -2.6027]","-2.6981<br/>[-2.6982, -2.6981]","-2.8153<br/>[-2.8153, -2.8149]","-2.9771<br/>[-2.9771, -2.9771]","-2.9970<br/>[-2.9970, -2.9961]","-3.2406<br/>[-3.2410, -3.2406]","-2.1099<br/>[-2.1099, -2.1099]","-1.7996<br/>[-1.8297, -1.7931]","-2.5217<br/>[-2.5300, -2.5217]","-2.1751<br/>[-2.1752, -2.1751]","-2.9946<br/>[-2.9946, -2.9946]","-3.0269<br/>[-3.0419, -3.0236]","-2.0647<br/>[-2.0649, -2.0647]","-2.7395<br/>[-2.7395, -2.7391]","-1.8905<br/>[-1.8905, -1.8905]","-2.3050<br/>[-2.3223, -2.3050]","-2.5384<br/>[-2.5385, -2.5367]","-3.1747<br/>[-3.1768, -3.1591]","-2.7057<br/>[-2.7804, -2.6979]","-3.2450<br/>[-3.2450, -3.2450]","-2.8095<br/>[-2.8095, -2.8092]","-3.1675<br/>[-3.1675, -3.1675]","-2.4283<br/>[-2.4284, -2.4283]","-2.4010<br/>[-2.4024, -2.3997]","-2.3380<br/>[-2.3490, -2.3314]","-2.9434<br/>[-2.9437, -2.9430]","-1.5140<br/>[-1.5140, -1.5140]","-2.8021<br/>[-2.8035, -2.8021]","-1.9367<br/>[-1.9369, -1.9366]","-2.3193<br/>[-2.3199, -2.3188]","-2.3840<br/>[-2.3843, -2.3838]","-2.9742<br/>[-2.9742, -2.9742]","-2.7503<br/>[-2.7607, -2.7446]","-3.1456<br/>[-3.1461, -3.1439]","-2.7154<br/>[-2.7154, -2.7152]","-3.2105<br/>[-3.2105, -3.2105]","-3.1898<br/>[-3.1918, -3.1886]","-3.1898<br/>[-3.1918, -3.1886]","-3.4673<br/>[-3.5103, -3.4276]","-3.1071<br/>[-3.1091, -3.1060]","-2.4152<br/>[-2.4152, -2.4152]","-3.6753<br/>[-3.7055, -3.6525]","-3.6904<br/>[-3.7822, -3.6260]","-3.7741<br/>[-3.9178, -3.6490]","-3.7855<br/>[-3.8915, -3.7144]","-3.7100<br/>[-3.8005, -3.6697]","-3.5502<br/>[-3.5515, -3.5493]","-3.9475<br/>[-3.9976, -3.8801]","-3.5115<br/>[-3.5120, -3.5112]","-3.3242<br/>[-4.0562, -3.2139]","-4.1665<br/>[-4.2481, -4.1146]","-4.3387<br/>[-5.3379, -4.0089]","-4.3387<br/>[-5.3379, -4.0089]","-6.0838<br/>[-6.9892, -5.6092]","-6.6139<br/>[-7.1959, -6.2525]","-6.4969<br/>[-7.3751, -6.0298]","-6.1462<br/>[-7.3086, -5.5980]","-6.6045<br/>[-7.3810, -6.1649]","-5.0352<br/>[-6.8414, -4.3676]","-6.4217<br/>[-7.4458, -5.8987]","-5.5511<br/>[-7.2702, -4.8750]","-5.6813<br/>[-7.3328, -5.0228]","-4.9778<br/>[-6.5213, -4.3722]","-5.4943<br/>[-7.2872, -4.7929]","-5.5833<br/>[-7.4361, -4.8845]","-4.7971<br/>[-6.4837, -4.1561]","-5.4540<br/>[-7.4335, -4.7472]","-5.2613<br/>[-7.3774, -4.5783]","-5.6958<br/>[-7.0284, -5.0694]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(database, repository)<\/th>\n <th># of genes<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 3, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-highly-expressed-genes" class="section level3">
<h3>Tissue highly expressed genes</h3>
<div id="htmlwidget-0aaad034f4771159c3b9" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-0aaad034f4771159c3b9">{"x":{"filter":"none","data":[["Artery - Tibial","Artery - Coronary","Artery - Aorta","Spleen","Small Intestine - Terminal Ileum","Lung","Cells - EBV-transformed lymphocytes","Colon - Transverse","Pancreas","Breast - Mammary Tissue","Nerve - Tibial","Brain - Cerebellum","Prostate","Adipose - Subcutaneous","Adrenal Gland","Esophagus - Mucosa","Brain - Cerebellar Hemisphere","Uterus","Vagina","Adipose - Visceral (Omentum)","Brain - Hippocampus","Brain - Cortex","Skin - Sun Exposed (Lower leg)","Esophagus - Gastroesophageal Junction","Ovary","Skin - Not Sun Exposed (Suprapubic)","Pituitary","Muscle - Skeletal","Brain - Hypothalamus","Brain - Anterior cingulate cortex (BA24)","Colon - Sigmoid","Esophagus - Muscularis","Cells - Transformed fibroblasts","Brain - Nucleus accumbens (basal ganglia)","Brain - Frontal Cortex (BA9)","Thyroid","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)","Stomach","Liver","Testis","Heart - Left Ventricle","Heart - Atrial Appendage","Whole Blood"],[6427,6564,6723,4312,5041,5349,5286,5591,5483,5971,6081,6060,5971,5999,6011,5984,6015,6057,6192,6250,6104,6226,6119,6159,6270,6192,6260,6038,6230,6304,6266,6358,6488,6488,6583,6553,6892,6969,5622,6705,6261,5958,6207,6265],[692.028257548677,691.977941221849,691.884814712882,690.576724327129,690.234080886651,690.096557006595,690.045743593701,689.9640573283,689.963218346045,689.797147729906,689.785908165876,689.767045010941,689.767029415765,689.765605770467,689.754135669849,689.742504772684,689.742386486844,689.737570621506,689.710825275857,689.697691479682,689.687310236015,689.681702817829,689.675200983401,689.662470891742,689.658737970102,689.653989335984,689.650373024546,689.642594192359,689.637020290694,689.615015324361,689.598703367909,689.582519311132,689.537536051396,689.50983704749,689.500082509252,689.487784254997,689.371970698877,689.298905213313,677.257272461302,534.240131009162,292.014004521002,7.01530114805197,6.94340457703642,1.376045364021],["-4.4381<br/>[-4.4381, -4.4381]","-4.4381<br/>[-4.4381, -4.4381]","-4.4380<br/>[-4.4380, -4.4380]","-4.4180<br/>[-4.4180, -4.4180]","-4.4177<br/>[-4.4177, -4.4177]","-4.4176<br/>[-4.4176, -4.4176]","-4.4176<br/>[-4.4176, -4.4176]","-4.4175<br/>[-4.4175, -4.4175]","-4.4175<br/>[-4.4175, -4.4175]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4172<br/>[-4.4172, -4.4172]","-4.4173<br/>[-4.4173, -4.4173]","-4.4172<br/>[-4.4172, -4.4172]","-4.4173<br/>[-4.4173, -4.4173]","-4.4173<br/>[-4.4173, -4.4173]","-4.4172<br/>[-4.4172, -4.4172]","-4.4173<br/>[-4.4173, -4.4173]","-4.4172<br/>[-4.4172, -4.4172]","-4.4173<br/>[-4.4173, -4.4173]","-4.4172<br/>[-4.4172, -4.4172]","-4.4172<br/>[-4.4172, -4.4172]","-4.4172<br/>[-4.4172, -4.4172]","-4.4172<br/>[-4.4172, -4.4172]","-4.4171<br/>[-4.4171, -4.4171]","-4.4171<br/>[-4.4171, -4.4171]","-4.4171<br/>[-4.4171, -4.4171]","-4.4171<br/>[-4.4171, -4.4171]","-4.4170<br/>[-4.4170, -4.4170]","-4.4169<br/>[-4.4169, -4.4169]","-4.4175<br/>[-4.4175, -4.4175]","-4.4171<br/>[-4.4171, -4.4171]","-4.4382<br/>[-4.4382, -4.4382]","-4.4475<br/>[-4.4475, -4.4475]","-4.4474<br/>[-4.4474, -4.4474]","-4.4260<br/>[-4.4260, -4.4260]"],["-2.9622<br/>[-2.9625, -2.9617]","-2.9713<br/>[-2.9716, -2.9709]","-2.9817<br/>[-2.9820, -2.9812]","-2.9354<br/>[-2.9355, -2.9351]","-3.0031<br/>[-3.0033, -3.0027]","-3.0290<br/>[-3.0291, -3.0287]","-3.0238<br/>[-3.0240, -3.0236]","-3.0481<br/>[-3.0483, -3.0478]","-3.0397<br/>[-3.0398, -3.0395]","-3.0768<br/>[-3.0769, -3.0765]","-3.0846<br/>[-3.0848, -3.0844]","-3.0831<br/>[-3.0833, -3.0829]","-3.0765<br/>[-3.0767, -3.0761]","-3.0788<br/>[-3.0789, -3.0786]","-3.0796<br/>[-3.0797, -3.0793]","-3.0776<br/>[-3.0778, -3.0774]","-3.0799<br/>[-3.0800, -3.0796]","-3.0830<br/>[-3.0831, -3.0828]","-3.0925<br/>[-3.0926, -3.0923]","-3.0966<br/>[-3.0967, -3.0964]","-3.0863<br/>[-3.0864, -3.0861]","-3.0947<br/>[-3.0949, -3.0944]","-3.0874<br/>[-3.0875, -3.0871]","-3.0902<br/>[-3.0903, -3.0900]","-3.0979<br/>[-3.0980, -3.0977]","-3.0925<br/>[-3.0926, -3.0923]","-3.0972<br/>[-3.0973, -3.0970]","-3.0815<br/>[-3.0816, -3.0812]","-3.0951<br/>[-3.0952, -3.0949]","-3.1002<br/>[-3.1003, -3.0999]","-3.0977<br/>[-3.0978, -3.0975]","-3.1040<br/>[-3.1041, -3.1038]","-3.1128<br/>[-3.1129, -3.1126]","-3.1128<br/>[-3.1129, -3.1126]","-3.1189<br/>[-3.1191, -3.1186]","-3.1172<br/>[-3.1173, -3.1170]","-3.1390<br/>[-3.1391, -3.1388]","-3.1438<br/>[-3.1440, -3.1436]","-3.0478<br/>[-3.0478, -3.0476]","-3.5248<br/>[-3.5253, -3.5240]","-2.9272<br/>[-2.9272, -2.9264]","-3.1953<br/>[-3.2806, -3.0958]","-3.2183<br/>[-3.2994, -3.1244]","-3.6396<br/>[-3.8331, -3.4640]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-selectively-expressed-genes" class="section level3">
<h3>Tissue selectively expressed genes</h3>
<div id="htmlwidget-9dd0ac780160f191cf9f" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9dd0ac780160f191cf9f">{"x":{"filter":"none","data":[["Pancreas","Nerve_Tibial","Adipose_Subcutaneous","Colon_Transverse","Small_Intestine_Terminal_Ileum","Testis","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis","Brain_Caudate_(basal_ganglia)","Liver","Brain_Putamen_(basal_ganglia)","Pituitary","Artery_Coronary","Cells_Transformed_fibroblasts","Adrenal_Gland","Brain_Cerebellum","Whole_Blood","Spleen","Brain_Cerebellar_Hemisphere","Lung","Heart_Left_Ventricle","Heart_Atrial_Appendage","Stomach","Artery_Aorta","Brain_Spinal_cord_(cervical_c-1)","Muscle_Skeletal","Ovary","Uterus","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Vagina","Esophagus_Mucosa","Cells_EBV-transformed_lymphocytes","Minor_Salivary_Gland","Prostate","Kidney_Cortex","Adipose_Visceral_(Omentum)","Breast_Mammary_Tissue","Thyroid","Colon_Sigmoid","Brain_Hippocampus","Brain_Amygdala","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Cortex","Brain_Hypothalamus","Artery_Tibial","Brain_Substantia_nigra","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Frontal_Cortex_(BA9)"],[8049,12991,10590,7975,9206,8188,14644,14813,12286,8581,12328,10043,12911,11213,12843,11394,7582,7631,14051,8812,11566,11642,9782,14917,13265,9069,12158,13051,7183,7260,7194,7271,8216,8945,9562,9460,10331,10321,12524,11407,11526,11765,11897,12558,12724,13070,13248,13644,14308],[2396.80780825469,1746.3923570272,1192.43326050561,807.701032803462,807.477376798116,758.853537704687,632.979637667092,632.532327759626,631.699463310025,534.039847618159,505.60844999472,324.710560288479,280.538375845117,185.135390173817,147.305520042619,124.955211277665,107.873713726961,99.7169582604406,97.6660778955263,30.8618779189198,10.3191585595917,5.98271848548219,4.5363606142724,3.15042963454891,-0.125596780285934,-0.137515764093574,-0.213892127310824,-0.231430921118576,-0.412600886735522,-0.413848714228055,-0.414208634918258,-0.41530839846704,-0.427442925629199,-0.429620050138592,-0.437263461683205,-0.439969014225794,-0.4480446016382,-0.4496194659372,-0.455075673018383,-0.45782566731469,-0.461009837774964,-0.462784727223381,-0.463920290853059,-0.469313875213965,-0.470933477304266,-0.473854012507256,-0.47556853542568,-0.478547124001553,-0.483851145125581],["-4.7154<br/>[-4.7154, -4.7154]","-4.4146<br/>[-4.4146, -4.4146]","-4.6557<br/>[-4.6557, -4.6557]","-4.4174<br/>[-4.4174, -4.4174]","-4.4170<br/>[-4.4170, -4.4170]","-4.4483<br/>[-4.4483, -4.4483]","-4.4353<br/>[-4.4353, -4.4353]","-4.4348<br/>[-4.4348, -4.4348]","-4.4358<br/>[-4.4358, -4.4358]","-4.4163<br/>[-4.4163, -4.4163]","-4.4357<br/>[-4.4357, -4.4357]","-4.4475<br/>[-4.4475, -4.4475]","-4.4576<br/>[-4.4576, -4.4576]","-4.4153<br/>[-4.4153, -4.4153]","-4.4356<br/>[-4.4356, -4.4356]","-4.4152<br/>[-4.4152, -4.4152]","-4.4254<br/>[-4.4254, -4.4254]","-4.4167<br/>[-4.4167, -4.4167]","-4.4142<br/>[-4.4142, -4.4142]","-4.4162<br/>[-4.4162, -4.4162]","-4.4453<br/>[-4.4453, -4.4453]","-4.4452<br/>[-4.4452, -4.4452]","-4.4212<br/>[-4.4212, -4.4212]","-4.4348<br/>[-4.4348, -4.4348]","-4.4145<br/>[-4.4145, -4.4145]","-4.4161<br/>[-4.4161, -4.4161]","-4.4149<br/>[-4.4149, -4.4149]","-4.4146<br/>[-4.4146, -4.4146]","-4.4169<br/>[-4.4169, -4.4169]","-4.4168<br/>[-4.4168, -4.4168]","-4.4169<br/>[-4.4169, -4.4169]","-4.4168<br/>[-4.4168, -4.4168]","-4.4165<br/>[-4.4165, -4.4165]","-4.4162<br/>[-4.4162, -4.4162]","-4.4159<br/>[-4.4159, -4.4159]","-4.4160<br/>[-4.4160, -4.4160]","-4.4156<br/>[-4.4156, -4.4156]","-4.4156<br/>[-4.4156, -4.4156]","-4.4148<br/>[-4.4148, -4.4148]","-4.4152<br/>[-4.4152, -4.4152]","-4.4152<br/>[-4.4152, -4.4152]","-4.4151<br/>[-4.4151, -4.4151]","-4.4150<br/>[-4.4150, -4.4150]","-4.4148<br/>[-4.4148, -4.4148]","-4.4147<br/>[-4.4147, -4.4147]","-4.4146<br/>[-4.4146, -4.4146]","-4.4145<br/>[-4.4145, -4.4145]","-4.4143<br/>[-4.4143, -4.4143]","-4.4141<br/>[-4.4141, -4.4141]"],["-2.3615<br/>[-2.3615, -2.3615]","-2.9111<br/>[-2.9111, -2.9111]","-2.5929<br/>[-2.5930, -2.5929]","-3.2994<br/>[-3.2996, -3.2991]","-3.3617<br/>[-3.3619, -3.3614]","-3.2130<br/>[-3.2139, -3.2120]","-3.0615<br/>[-3.0682, -3.0569]","-3.0905<br/>[-3.0910, -3.0900]","-3.0091<br/>[-3.0101, -3.0085]","-3.6320<br/>[-3.6324, -3.6314]","-3.0106<br/>[-3.0111, -3.0097]","-3.1555<br/>[-3.1558, -3.1554]","-3.4117<br/>[-3.4119, -3.4115]","-3.3300<br/>[-3.3300, -3.3295]","-3.5063<br/>[-3.5065, -3.5060]","-2.0328<br/>[-2.0328, -2.0328]","-1.9803<br/>[-1.9803, -1.9803]","-1.9891<br/>[-1.9891, -1.9891]","-2.0259<br/>[-2.0259, -2.0259]","-1.9162<br/>[-1.9162, -1.9162]","-3.3997<br/>[-3.4515, -3.3407]","-3.5358<br/>[-3.5821, -3.4748]","-3.6459<br/>[-3.6858, -3.5872]","-3.8218<br/>[-3.8705, -3.7562]","-4.3337<br/>[-5.4018, -4.0747]","-4.2191<br/>[-5.5144, -3.9133]","-4.3901<br/>[-5.5314, -4.0458]","-4.4291<br/>[-5.5610, -4.0692]","-5.8014<br/>[-7.4454, -5.1338]","-5.8288<br/>[-7.4676, -5.1856]","-5.9641<br/>[-7.6058, -5.3197]","-5.9809<br/>[-7.6180, -5.3310]","-6.0858<br/>[-7.6808, -5.4419]","-5.6535<br/>[-7.1080, -5.0154]","-5.7153<br/>[-7.2034, -5.0635]","-5.9713<br/>[-7.5085, -5.3325]","-5.9249<br/>[-7.4438, -5.2836]","-6.1018<br/>[-7.6155, -5.4524]","-5.4485<br/>[-6.9131, -4.7840]","-5.9339<br/>[-7.4144, -5.2812]","-6.1452<br/>[-7.6284, -5.5104]","-6.1078<br/>[-7.5861, -5.4660]","-6.1083<br/>[-7.5825, -5.4618]","-6.0958<br/>[-7.5538, -5.4583]","-6.1258<br/>[-7.5783, -5.4815]","-6.1438<br/>[-7.5891, -5.5181]","-6.1806<br/>[-7.6179, -5.5480]","-6.1695<br/>[-7.5983, -5.5252]","-6.2067<br/>[-7.6198, -5.5720]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="cluster-distinctively-expressed-genes" class="section level3">
<h3>Cluster distinctively expressed genes</h3>
<div id="htmlwidget-798b325e8770e69abc2e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-798b325e8770e69abc2e">{"x":{"filter":"none","data":[["11","20","8","13","10","7","2","1","14","5","17","9","4","19","12","18","15","6","3","16"],[10805,8521,10547,7915,8809,8610,9326,7787,9748,11872,8920,9916,12796,6176,7539,7654,8110,9259,10492,10617],[1658.63652000691,534.055370218329,170.366833898067,158.978971625693,148.671960535662,130.619592572912,99.0398025943116,26.9384555637681,6.29421228266856,3.38625805976331,2.53417894181975,2.34265810831986,0.0261470471532334,-0.395558563048842,-0.408402890159809,-0.41538732283637,-0.421437149910261,-0.432677725736911,-0.44678752478931,-0.447280945128102],["-4.4258<br/>[-4.4258, -4.4258]","-4.4163<br/>[-4.4163, -4.4163]","-4.4156<br/>[-4.4156, -4.4156]","-4.4376<br/>[-4.4376, -4.4376]","-4.4458<br/>[-4.4458, -4.4458]","-4.4163<br/>[-4.4163, -4.4163]","-4.4370<br/>[-4.4370, -4.4370]","-4.4166<br/>[-4.4166, -4.4166]","-4.4460<br/>[-4.4460, -4.4460]","-4.4360<br/>[-4.4360, -4.4360]","-4.4255<br/>[-4.4255, -4.4255]","-4.4240<br/>[-4.4240, -4.4240]","-4.4151<br/>[-4.4151, -4.4151]","-4.4173<br/>[-4.4173, -4.4173]","-4.4167<br/>[-4.4167, -4.4167]","-4.4167<br/>[-4.4167, -4.4167]","-4.4165<br/>[-4.4165, -4.4165]","-4.4161<br/>[-4.4161, -4.4161]","-4.4156<br/>[-4.4156, -4.4156]","-4.4155<br/>[-4.4155, -4.4155]"],["-2.8053<br/>[-2.8053, -2.8053]","-3.6291<br/>[-3.6294, -3.6287]","-3.2359<br/>[-3.2359, -3.2351]","-1.8463<br/>[-1.8487, -1.8463]","-3.2490<br/>[-3.2520, -3.2472]","-3.1716<br/>[-3.1725, -3.1628]","-1.8502<br/>[-1.8502, -1.8502]","-3.5523<br/>[-3.5867, -3.5009]","-3.4334<br/>[-3.4966, -3.3376]","-3.7094<br/>[-3.7669, -3.6312]","-3.5386<br/>[-3.6737, -3.4259]","-3.6741<br/>[-3.7488, -3.6145]","-4.0930<br/>[-5.3683, -3.7800]","-5.8411<br/>[-7.5360, -5.1630]","-5.5738<br/>[-7.0291, -4.9242]","-5.9043<br/>[-7.5232, -5.2535]","-5.9853<br/>[-7.5835, -5.3071]","-5.8722<br/>[-7.4104, -5.2040]","-6.0764<br/>[-7.5813, -5.4069]","-6.0021<br/>[-7.5043, -5.3316]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Cluster ID<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
<p>The relationship between tissues and clusters is shown in Figure 1 of <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006599">Dey et al. (2017)</a>; see below.</p>
<p><img src="http://journals.plos.org/plosgenetics/article/figure/image?size=large&id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">devtools<span class="op">::</span><span class="kw">session_info</span>()</a></code></pre></div>
<pre><code>Session info -------------------------------------------------------------</code></pre>
<pre><code> setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-10-05 </code></pre>
<pre><code>Packages -----------------------------------------------------------------</code></pre>
<pre><code> package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.1 2018-07-05 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.5.0)
compiler 3.5.1 2018-07-05 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
crosstalk 1.0.0 2016-12-21 CRAN (R 3.5.0)
datasets * 3.5.1 2018-07-05 local
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.0)
dplyr * 0.7.6 2018-06-29 CRAN (R 3.5.1)
DT * 0.4 2018-01-30 CRAN (R 3.5.0)
evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 CRAN (R 3.5.0)
graphics * 3.5.1 2018-07-05 local
grDevices * 3.5.1 2018-07-05 local
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
htmlwidgets 1.3 2018-09-30 CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
later 0.7.5 2018-09-18 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.1 2018-07-05 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.5.0)
promises 1.0.1 2018-04-13 CRAN (R 3.5.0)
purrr 0.2.5 2018-05-29 CRAN (R 3.5.0)
R.matlab * 3.6.2 2018-09-27 CRAN (R 3.5.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.5.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.5.0)
R.utils 2.7.0 2018-08-27 CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 CRAN (R 3.5.0)
Rcpp 0.12.19 2018-10-01 CRAN (R 3.5.0)
rlang 0.2.2 2018-08-16 CRAN (R 3.5.0)
rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
shiny 1.1.0 2018-05-17 CRAN (R 3.5.0)
stats * 3.5.1 2018-07-05 local
stringi 1.2.4 2018-07-20 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tools 3.5.1 2018-07-05 local
utils * 3.5.1 2018-07-05 local
whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
workflowr 1.1.1 2018-07-06 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)</code></pre>
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