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<h1 class="title toc-ignore">Enrichment results of low-density lipoprotein</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> 2018-07-02</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/20686565">“Biological, Clinical and Population Relevance of 95 Loci for Blood Lipids” (<em>Nature</em>, 2010)</a>. The summary data file is available at <a href="http://csg.sph.umich.edu/willer/public/lipids2010" class="uri">http://csg.sph.umich.edu/willer/public/lipids2010</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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expression<br/>(biocarta, BioCarta)","Scavenging by Class A Receptors<br/>(reactome, PC)","HDL-mediated lipid transport<br/>(reactome, PC)","Binding and Uptake of Ligands by Scavenger Receptors<br/>(reactome, BioSystems)","Binding and Uptake of Ligands by Scavenger Receptors<br/>(reactome, PC)","Diseases associated with visual transduction<br/>(reactome, PC)","Visual phototransduction<br/>(reactome, BioSystems)","Vitamin B12 Metabolism<br/>(wiki, BioSystems)","Scavenging by Class B Receptors<br/>(reactome, PC)","Atypical NF-kappaB pathway<br/>(pid, PC)","Golgi Associated Vesicle Biogenesis<br/>(reactome, PC)","Clathrin derived vesicle budding<br/>(reactome, PC)","Clathrin derived vesicle budding<br/>(reactome, BioSystems)","Organic cation/anion/zwitterion transport<br/>(reactome, BioSystems)","TNF-alpha/NF-kB Signaling Pathway<br/>(wiki, BioSystems)","Nectin adhesion pathway<br/>(pid, BioSystems)","Monoamine Transport<br/>(wiki, BioSystems)","FXR and LXR Regulation of Cholesterol 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lateral sclerosis (ALS)<br/>(kegg, BioSystems)","Cell-cell junction organization<br/>(reactome, PC)","Aminoacyl-tRNA biosynthesis<br/>(kegg, BioSystems)","tRNA charging<br/>(humancyc, PC)","formation of the beta-catenin:TCF transactivating complex<br/>(reactome, PC)","Aminoacyl-tRNA biosynthesis, eukaryotes<br/>(kegg, BioSystems)","tRNA Aminoacylation<br/>(reactome, PC)","Factors involved in megakaryocyte development and platelet production<br/>(reactome, PC)","Factors involved in megakaryocyte development and platelet production<br/>(reactome, BioSystems)","Glucocorticoid receptor regulatory network<br/>(pid, PC)","Neurotrophin signaling pathway<br/>(kegg, BioSystems)","Lysosome<br/>(kegg, BioSystems)","BDNF signaling pathway<br/>(wiki, BioSystems)","Bacterial invasion of epithelial cells<br/>(kegg, BioSystems)","Fatty acid, triacylglycerol, and ketone body metabolism<br/>(reactome, PC)","T cell receptor signaling pathway<br/>(kegg, BioSystems)","EGF receptor signaling pathway<br/>(panther, PANTHER)","EGF receptor signaling pathway<br/>(panther, PC)","Gap junction trafficking and regulation<br/>(reactome, PC)","p75(NTR)-mediated signaling<br/>(pid, BioSystems)","p75(NTR)-mediated signaling<br/>(pid, PC)","ErbB signaling pathway<br/>(kegg, BioSystems)","Cell junction organization<br/>(reactome, PC)","Cell junction organization<br/>(reactome, BioSystems)","Fatty acid, triacylglycerol, and ketone body metabolism<br/>(reactome, BioSystems)","Herpes simplex infection<br/>(kegg, BioSystems)","Cell-Cell communication<br/>(reactome, PC)","Cell-Cell communication<br/>(reactome, BioSystems)","Adherens junction<br/>(kegg, BioSystems)","Insulin signaling pathway<br/>(kegg, BioSystems)","Cell adhesion molecules (CAMs)<br/>(kegg, BioSystems)"],[17,30,5,6,18,30,50,58,39,6,103,7,5,231,39,40,4,19,15,40,41,88,89,19,5,14,49,56,65,14,181,25,31,7,184,169,490,496,193,30,14,69,85,6,6,93,25,2,7,3,2,70,47,4,52,49,108,41,9,96,71,252,24,40,42,16,61,30,23,51,59,44,37,86,38,42,133,134,82,115,117,136,76,174,101,99,108,29,55,62,84,82,83,181,174,126,127,72,133,134],[1139,2311,489,486,1041,2618,3959,4463,3328,512,8279,665,389,19646,4541,4541,541,2338,1460,4171,4231,8917,8917,1505,506,1178,4536,4869,5666,1274,14394,2892,2987,705,14843,15633,45889,46250,15723,3415,1205,3435,6860,569,527,4488,3048,153,673,217,262,7366,3284,281,6444,3304,9398,2630,1088,8626,6425,22188,1846,4323,4538,1424,5236,5579,1808,4924,8006,3603,2970,3268,3062,3457,10328,10406,6707,10587,9100,14423,8696,17074,8904,10953,11687,2036,4590,5121,9785,10550,10550,17634,10783,17214,17214,9483,10995,14575],[65.5286624690027,63.9837738149057,59.8797570588217,59.73479824713,59.0653361166729,56.6878806592324,54.8308688379987,51.6830873839095,48.7388497147727,43.1581751272986,41.871735891333,34.5057544822095,34.0158074473022,34.0014596468015,33.9252369926093,33.9252369926093,33.8113592928551,30.5316948406917,30.2165240874165,30.1592842082679,29.7146171695189,27.134310164359,27.134310164359,26.9666542728607,25.8022576229393,24.6705223194266,23.0397853333724,22.7491253050679,21.6917692865133,19.9059845639386,18.1142382241471,17.9328682169879,17.5155358960695,16.7509830376869,16.5581616732514,16.4413439557194,16.3714941179733,16.2988043553166,16.0757663832413,16.0111113924227,15.5080364392251,15.4927708793939,15.3364756538234,15.1713752075767,14.5531240157203,14.5502944485425,14.5214913740828,14.4488367051166,14.377852565475,14.2010454066907,14.0376472579907,14.0327300437947,13.997924734111,13.970411418755,13.955440632834,13.9388253704654,13.8020954844745,13.8006498191217,13.7897046035896,13.6735683513346,13.4496389040791,13.3863942629125,12.9905103110063,12.9677839061592,12.857923409555,12.7867460606507,12.4257202085483,12.4197263932258,12.3709853727834,12.217200394721,11.9003803889121,11.5685870342031,11.5590014519879,11.5472442994237,11.4740001858512,11.4131009795859,11.2746188139444,11.2542371476551,11.1963723167759,11.088652036022,10.9911187232654,10.8164686367659,10.6968967540769,10.591947256885,10.2722965086959,10.2676885603383,10.19035646881,10.188256652565,10.1222510998736,9.9632166354649,9.71573777929333,9.30849739344155,9.30849739344155,8.88574816564796,8.70610600810732,8.44426320147171,8.44426320147171,8.18968988728376,7.53215266414573,5.74065586244143],["-3.7788<br/>[-3.7796, -3.7607]","-3.7963<br/>[-3.7972, -3.7776]","-3.7176<br/>[-3.7183, -3.7018]","-3.7237<br/>[-3.7244, -3.7077]","-3.7175<br/>[-3.7182, -3.7017]","-3.7891<br/>[-3.7899, -3.7706]","-3.7996<br/>[-3.8005, -3.7808]","-3.7998<br/>[-3.8007, -3.7809]","-3.7172<br/>[-3.7179, -3.7014]","-3.7453<br/>[-3.7461, -3.7285]","-3.7188<br/>[-3.7195, -3.7030]","-3.7566<br/>[-3.7574, -3.7394]","-3.7178<br/>[-3.7185, -3.7020]","-3.7904<br/>[-3.7912, -3.7721]","-3.7750<br/>[-3.7758, -3.7570]","-3.7750<br/>[-3.7758, -3.7570]","-3.7182<br/>[-3.7190, -3.7024]","-3.7606<br/>[-3.7614, -3.7432]","-3.7584<br/>[-3.7592, -3.7411]","-3.7658<br/>[-3.7666, -3.7483]","-3.7658<br/>[-3.7666, -3.7483]","-3.7762<br/>[-3.7770, -3.7583]","-3.7762<br/>[-3.7770, -3.7583]","-3.7534<br/>[-3.7542, -3.7363]","-3.7281<br/>[-3.7289, -3.7120]","-3.7310<br/>[-3.7318, -3.7148]","-3.7368<br/>[-3.7376, -3.7205]","-3.7368<br/>[-3.7375, -3.7204]","-3.7366<br/>[-3.7373, -3.7202]","-3.7279<br/>[-3.7287, -3.7118]","-3.7565<br/>[-3.7573, -3.7392]","-3.7585<br/>[-3.7593, -3.7412]","-3.7515<br/>[-3.7523, -3.7344]","-3.7310<br/>[-3.7318, -3.7148]","-3.7390<br/>[-3.7398, -3.7227]","-3.7648<br/>[-3.7656, -3.7474]","-3.7423<br/>[-3.7431, -3.7258]","-3.7422<br/>[-3.7430, -3.7257]","-3.7388<br/>[-3.7395, -3.7224]","-3.7583<br/>[-3.7591, -3.7410]","-3.7286<br/>[-3.7294, -3.7124]","-3.7565<br/>[-3.7573, -3.7393]","-3.7405<br/>[-3.7413, -3.7239]","-3.7294<br/>[-3.7302, -3.7132]","-3.7288<br/>[-3.7296, -3.7126]","-3.7562<br/>[-3.7571, -3.7391]","-3.7242<br/>[-3.7250, -3.7082]","-3.7176<br/>[-3.7184, -3.7018]","-3.7258<br/>[-3.7265, -3.7097]","-3.7176<br/>[-3.7184, -3.7018]","-3.7176<br/>[-3.7184, -3.7018]","-3.7490<br/>[-3.7498, -3.7321]","-3.7512<br/>[-3.7520, -3.7341]","-3.7176<br/>[-3.7183, -3.7018]","-3.7485<br/>[-3.7493, -3.7316]","-3.7512<br/>[-3.7520, -3.7341]","-3.7323<br/>[-3.7331, -3.7160]","-3.7418<br/>[-3.7426, -3.7252]","-3.7280<br/>[-3.7287, -3.7118]","-3.7414<br/>[-3.7422, -3.7248]","-3.7492<br/>[-3.7500, -3.7323]","-3.7711<br/>[-3.7719, -3.7535]","-3.7239<br/>[-3.7247, -3.7079]","-3.7487<br/>[-3.7495, -3.7317]","-3.7486<br/>[-3.7494, -3.7317]","-3.7333<br/>[-3.7341, -3.7169]","-3.7352<br/>[-3.7360, -3.7189]","-3.7555<br/>[-3.7563, -3.7383]","-3.7235<br/>[-3.7243, -3.7075]","-3.7487<br/>[-3.7495, -3.7318]","-3.7566<br/>[-3.7574, -3.7394]","-3.7236<br/>[-3.7243, -3.7076]","-3.7234<br/>[-3.7242, -3.7074]","-3.7307<br/>[-3.7314, -3.7144]","-3.7234<br/>[-3.7241, -3.7074]","-3.7234<br/>[-3.7242, -3.7075]","-3.7271<br/>[-3.7279, -3.7110]","-3.7271<br/>[-3.7278, -3.7110]","-3.7295<br/>[-3.7303, -3.7133]","-3.7257<br/>[-3.7265, -3.7096]","-3.7291<br/>[-3.7299, -3.7129]","-3.7251<br/>[-3.7258, -3.7090]","-3.7478<br/>[-3.7486, -3.7309]","-3.7395<br/>[-3.7403, -3.7230]","-3.7498<br/>[-3.7506, -3.7329]","-3.7506<br/>[-3.7514, -3.7336]","-3.7508<br/>[-3.7516, -3.7339]","-3.7193<br/>[-3.7201, -3.7035]","-3.7212<br/>[-3.7219, -3.7053]","-3.7211<br/>[-3.7219, -3.7052]","-3.7499<br/>[-3.7507, -3.7329]","-3.7590<br/>[-3.7598, -3.7417]","-3.7590<br/>[-3.7598, -3.7417]","-3.7393<br/>[-3.7401, -3.7229]","-3.7500<br/>[-3.7508, -3.7330]","-3.7599<br/>[-3.7607, -3.7426]","-3.7599<br/>[-3.7607, -3.7426]","-3.7478<br/>[-3.7486, -3.7309]","-3.7512<br/>[-3.7520, -3.7343]","-3.7546<br/>[-3.7554, -3.7375]"],["-1.2774<br/>[-1.2834, -1.2627]","-1.5392<br/>[-1.5725, -1.4891]","-2.1751<br/>[-2.3789, -2.1112]","-1.7521<br/>[-1.8271, -1.6890]","-2.6078<br/>[-2.6971, -2.5064]","-1.5831<br/>[-1.6058, -1.5154]","-1.7202<br/>[-1.7509, -1.6675]","-1.7801<br/>[-1.8697, -1.7114]","-2.8635<br/>[-2.9826, -2.7611]","-1.1480<br/>[-1.1974, -1.1065]","-2.7614<br/>[-2.7742, -2.7353]","-1.2916<br/>[-1.3364, -1.2628]","-1.9469<br/>[-2.0776, -1.8377]","-2.4246<br/>[-2.4904, -2.4071]","-2.0417<br/>[-2.0922, -2.0028]","-2.0417<br/>[-2.0922, -2.0028]","-2.0093<br/>[-2.2232, -1.8654]","-1.8387<br/>[-1.8849, -1.8228]","-1.6577<br/>[-1.6862, -1.6247]","-2.0253<br/>[-2.0752, -1.9878]","-2.0302<br/>[-2.0775, -1.9906]","-2.2859<br/>[-2.3353, -2.2584]","-2.2859<br/>[-2.3353, -2.2584]","-1.7118<br/>[-1.7320, -1.6801]","-1.5484<br/>[-1.6171, -1.3922]","-1.7628<br/>[-1.8119, -1.7139]","-2.2895<br/>[-2.3293, -2.2709]","-2.2888<br/>[-2.3691, -2.2358]","-2.3737<br/>[-2.4199, -2.3468]","-1.9347<br/>[-1.9360, -1.9219]","-2.5498<br/>[-2.5749, -2.5145]","-1.9092<br/>[-1.9806, -1.8416]","-2.0773<br/>[-2.0892, -2.0297]","-1.5895<br/>[-1.6309, -1.5648]","-2.6662<br/>[-2.6909, -2.6253]","-2.4905<br/>[-2.5256, -2.4715]","-3.0648<br/>[-3.0990, -3.0185]","-3.0679<br/>[-3.1015, -3.0207]","-2.6929<br/>[-2.7174, -2.6513]","-2.0394<br/>[-2.1404, -1.9773]","-2.0020<br/>[-2.1486, -1.9309]","-2.0182<br/>[-2.1592, -1.9627]","-2.4105<br/>[-2.4761, -2.3439]","-1.5524<br/>[-1.6058, -1.4724]","-1.7202<br/>[-1.9652, -1.4629]","-2.2429<br/>[-2.2543, -2.2264]","-2.5758<br/>[-2.7325, -2.4517]","-1.8148<br/>[-1.8809, -1.7369]","-1.8295<br/>[-1.8795, -1.7715]","-1.9436<br/>[-2.0311, -1.8467]","-2.0256<br/>[-2.1141, -1.9311]","-2.5025<br/>[-2.5613, -2.4557]","-2.1319<br/>[-2.1443, -2.0872]","-2.0606<br/>[-2.1435, -1.9671]","-2.3724<br/>[-2.4017, -2.3357]","-2.1341<br/>[-2.1680, -2.1066]","-2.5809<br/>[-2.6421, -2.5270]","-2.0826<br/>[-2.1357, -1.9849]","-1.8510<br/>[-1.8636, -1.8266]","-2.4590<br/>[-2.4953, -2.4131]","-2.3175<br/>[-2.3817, -2.2394]","-2.6405<br/>[-2.7033, -2.5950]","-2.3083<br/>[-2.4314, -2.2133]","-2.3206<br/>[-2.3476, -2.2064]","-2.3428<br/>[-2.3599, -2.3026]","-2.0147<br/>[-2.0991, -1.9418]","-2.3621<br/>[-2.4412, -2.2883]","-2.3351<br/>[-2.3494, -2.3277]","-2.3861<br/>[-2.5133, -2.2403]","-2.3926<br/>[-2.4080, -2.3689]","-2.4601<br/>[-2.4627, -2.4579]","-2.6208<br/>[-2.7378, -2.5228]","-2.5673<br/>[-2.6784, -2.4759]","-2.6103<br/>[-2.7376, -2.5066]","-2.5835<br/>[-2.6910, -2.4903]","-2.6035<br/>[-2.7315, -2.5038]","-2.9956<br/>[-3.1220, -2.9119]","-2.9995<br/>[-3.1230, -2.9143]","-2.8022<br/>[-2.8920, -2.7188]","-3.0625<br/>[-3.1094, -2.9884]","-2.8461<br/>[-2.9593, -2.7478]","-3.1098<br/>[-3.1445, -3.0494]","-2.4413<br/>[-2.4798, -2.4001]","-2.7519<br/>[-2.7525, -2.7506]","-2.4768<br/>[-2.5259, -2.4322]","-2.5229<br/>[-2.5725, -2.4768]","-2.5361<br/>[-2.5847, -2.4883]","-1.7398<br/>[-1.7398, -1.7397]","-2.7993<br/>[-2.9158, -2.7021]","-2.8378<br/>[-2.9531, -2.7335]","-2.5101<br/>[-2.5640, -2.4672]","-2.5258<br/>[-2.5365, -2.4890]","-2.5258<br/>[-2.5365, -2.4890]","-2.7452<br/>[-2.7659, -2.6773]","-2.5766<br/>[-2.6519, -2.5480]","-2.6648<br/>[-2.7278, -2.6523]","-2.6648<br/>[-2.7278, -2.6523]","-2.6625<br/>[-2.6961, -2.5677]","-2.5501<br/>[-2.5924, -2.5290]","-2.7183<br/>[-2.7750, -2.6386]"]],"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":[["Liver","Adrenal Gland","Brain - Cerebellum","Brain - Cortex","Brain - Anterior cingulate cortex (BA24)","Brain - Frontal Cortex (BA9)","Brain - Caudate (basal ganglia)","Brain - Hippocampus","Brain - Hypothalamus","Brain - Nucleus accumbens (basal ganglia)","Brain - Putamen (basal ganglia)","Prostate","Pituitary","Uterus","Cells - EBV-transformed lymphocytes","Testis","Small Intestine - Terminal Ileum","Pancreas","Vagina","Skin - Sun Exposed (Lower leg)","Breast - Mammary Tissue","Skin - Not Sun Exposed (Suprapubic)","Cells - Transformed fibroblasts","Ovary","Brain - Cerebellar Hemisphere","Esophagus - Mucosa","Colon - Transverse","Esophagus - Muscularis","Artery - Coronary","Stomach","Esophagus - Gastroesophageal Junction","Colon - Sigmoid","Artery - Tibial","Artery - Aorta","Spleen","Heart - Atrial Appendage","Lung","Adipose - Subcutaneous","Heart - Left Ventricle","Adipose - Visceral (Omentum)","Nerve - Tibial","Thyroid","Muscle - Skeletal","Whole Blood"],[6031,5349,5375,5537,5624,5907,6189,5476,5626,5826,6256,5307,5604,5394,4730,5542,4468,4865,5494,5417,5295,5478,5827,5583,5355,5335,4954,5712,5881,5001,5522,5620,5761,6048,3831,5534,4765,5356,5326,5547,5408,5873,5338,5592],[21.4578019405333,15.1672217498984,13.7816714810347,12.4550511323185,12.3474155748387,12.0083834906341,11.8788244346006,11.7038143243531,11.6340140518975,11.3957528881788,11.1790822101452,1.62886415429628,1.56286294480845,1.50596887492392,1.49901040341518,1.49268942102397,1.2983885512164,1.2901543990953,0.964019482032602,0.884069370835655,0.70456756535334,0.650232256300225,0.569099852269415,0.465304531066982,0.302975391241404,0.106148661809763,0.0170223478776234,-0.00781711734942957,-0.0285619240058373,-0.0372114266807462,-0.0623353664627131,-0.0839274612820607,-0.123805695944385,-0.18007423906167,-0.246101534105525,-0.382041067322732,-0.399015228312724,-0.439093059386931,-0.439111723051002,-0.450610422956152,-0.462693952488546,-0.525683532279535,-0.707018936321186,-0.744797049090938],["-3.7600<br/>[-3.7608, -3.7429]","-3.7557<br/>[-3.7565, -3.7385]","-3.7524<br/>[-3.7532, -3.7354]","-3.7499<br/>[-3.7507, -3.7330]","-3.7499<br/>[-3.7507, -3.7330]","-3.7498<br/>[-3.7506, -3.7328]","-3.7483<br/>[-3.7491, -3.7314]","-3.7485<br/>[-3.7493, -3.7315]","-3.7485<br/>[-3.7493, -3.7315]","-3.7483<br/>[-3.7491, -3.7314]","-3.7483<br/>[-3.7491, -3.7314]","-3.7238<br/>[-3.7246, -3.7079]","-3.7242<br/>[-3.7249, -3.7082]","-3.7231<br/>[-3.7238, -3.7071]","-3.7229<br/>[-3.7237, -3.7070]","-3.7198<br/>[-3.7205, -3.7040]","-3.7209<br/>[-3.7216, -3.7050]","-3.7232<br/>[-3.7239, -3.7072]","-3.7221<br/>[-3.7228, -3.7062]","-3.7228<br/>[-3.7235, -3.7068]","-3.7216<br/>[-3.7223, -3.7057]","-3.7230<br/>[-3.7237, -3.7071]","-3.7216<br/>[-3.7223, -3.7057]","-3.7232<br/>[-3.7240, -3.7073]","-3.7203<br/>[-3.7210, -3.7044]","-3.7176<br/>[-3.7183, -3.7018]","-3.7172<br/>[-3.7179, -3.7014]","-3.7173<br/>[-3.7180, -3.7016]","-3.7173<br/>[-3.7180, -3.7016]","-3.7171<br/>[-3.7178, -3.7013]","-3.7171<br/>[-3.7178, -3.7013]","-3.7171<br/>[-3.7178, -3.7013]","-3.7169<br/>[-3.7177, -3.7012]","-3.7169<br/>[-3.7176, -3.7011]","-3.7174<br/>[-3.7181, -3.7016]","-3.7189<br/>[-3.7196, -3.7030]","-3.7172<br/>[-3.7179, -3.7014]","-3.7171<br/>[-3.7179, -3.7014]","-3.7183<br/>[-3.7190, -3.7025]","-3.7171<br/>[-3.7179, -3.7014]","-3.7171<br/>[-3.7178, -3.7013]","-3.7169<br/>[-3.7177, -3.7012]","-3.7168<br/>[-3.7175, -3.7010]","-3.7167<br/>[-3.7174, -3.7009]"],["-2.2306<br/>[-2.2702, -2.1915]","-2.2409<br/>[-2.3385, -2.1891]","-2.3396<br/>[-2.4116, -2.2850]","-2.3972<br/>[-2.4472, -2.3318]","-2.4085<br/>[-2.4564, -2.3442]","-2.4387<br/>[-2.4733, -2.3754]","-2.4609<br/>[-2.4880, -2.3907]","-2.4279<br/>[-2.4650, -2.3616]","-2.4400<br/>[-2.4739, -2.3715]","-2.4646<br/>[-2.4868, -2.4035]","-2.4900<br/>[-2.5116, -2.4336]","-2.7626<br/>[-2.8527, -2.6854]","-2.7846<br/>[-2.9100, -2.7431]","-2.7945<br/>[-2.8847, -2.7071]","-2.7443<br/>[-2.8832, -2.7052]","-2.8002<br/>[-2.9371, -2.6879]","-2.7836<br/>[-2.9206, -2.6691]","-2.7992<br/>[-2.9439, -2.6886]","-2.8232<br/>[-2.9937, -2.7503]","-2.8666<br/>[-2.9427, -2.7829]","-2.8547<br/>[-3.0296, -2.7370]","-2.8606<br/>[-2.9888, -2.7923]","-2.9032<br/>[-3.0690, -2.7637]","-2.8941<br/>[-3.0115, -2.8692]","-2.9669<br/>[-3.1526, -2.8357]","-2.9932<br/>[-3.2183, -2.8272]","-3.0265<br/>[-3.1965, -2.8826]","-3.0449<br/>[-3.2283, -2.8914]","-3.0544<br/>[-3.2373, -2.9009]","-3.0495<br/>[-3.2057, -2.9117]","-3.0620<br/>[-3.2303, -2.9117]","-3.0715<br/>[-3.2373, -2.9223]","-3.0843<br/>[-3.2560, -2.9357]","-3.1096<br/>[-3.2750, -2.9628]","-3.0752<br/>[-3.2663, -2.9085]","-3.1785<br/>[-3.3283, -3.0230]","-3.1623<br/>[-3.3440, -2.9866]","-3.1874<br/>[-3.3728, -3.0095]","-3.1945<br/>[-3.3609, -3.0277]","-3.1937<br/>[-3.3874, -3.0149]","-3.2015<br/>[-3.3811, -3.0247]","-3.2422<br/>[-3.4093, -3.0715]","-3.3607<br/>[-3.5161, -3.1756]","-3.3912<br/>[-3.5357, -3.2053]"]],"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":[["Liver","Kidney_Cortex","Heart_Atrial_Appendage","Adrenal_Gland","Adipose_Subcutaneous","Small_Intestine_Terminal_Ileum","Adipose_Visceral_(Omentum)","Stomach","Minor_Salivary_Gland","Breast_Mammary_Tissue","Colon_Transverse","Brain_Cortex","Brain_Frontal_Cortex_(BA9)","Prostate","Brain_Nucleus_accumbens_(basal_ganglia)","Esophagus_Mucosa","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Cerebellum","Pancreas","Brain_Hippocampus","Ovary","Esophagus_Gastroesophageal_Junction","Brain_Amygdala","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Brain_Hypothalamus","Spleen","Artery_Aorta","Brain_Substantia_nigra","Whole_Blood","Esophagus_Muscularis","Artery_Tibial","Uterus","Heart_Left_Ventricle","Vagina","Cells_EBV-transformed_lymphocytes","Colon_Sigmoid","Artery_Coronary","Testis","Muscle_Skeletal","Thyroid","Lung","Pituitary","Brain_Cerebellar_Hemisphere","Cells_Transformed_fibroblasts","Nerve_Tibial","Brain_Spinal_cord_(cervical_c-1)"],[7790,8530,10618,11741,9689,8304,9373,8830,7990,9381,7128,11451,13135,8687,10873,6502,11195,11270,12460,10438,7317,10467,11076,13550,10733,6453,6537,11697,6811,13733,12194,6762,13725,12065,11999,10521,6398,7416,10500,11883,7339,8241,11516,7931,9084,13039,10323,11949,12168],[33.412024880446,8.51155122859739,8.36088822811218,7.72106662155477,1.75638369659217,0.768068518468028,0.574262061364489,0.088853445593211,-0.329292324088027,-0.386675266708668,-0.397100718139291,-0.446260165950369,-0.607549983046995,-0.670542067406141,-0.714923799570992,-0.71561344082355,-0.721833445946529,-0.74076463780338,-0.787156730479312,-0.859039523147883,-0.866759171479289,-0.911478772351024,-0.921289177246062,-0.930385904095957,-0.933022346974829,-0.960409886863702,-0.963001274832559,-0.967717267357328,-1.00184099927729,-1.00453323428705,-1.01008581453462,-1.03867978371957,-1.06595215459251,-1.07132853022051,-1.07483015271157,-1.07702459068192,-1.08334328716035,-1.09106426608409,-1.09243705390478,-1.11884282434952,-1.1248974166387,-1.12679918282616,-1.14105885434247,-1.15935741605709,-1.17504379191839,-1.17938386002736,-1.18096586539214,-1.19017455364736,-1.26138548300654],["-3.7749<br/>[-3.7757, -3.7573]","-3.7432<br/>[-3.7440, -3.7265]","-3.7218<br/>[-3.7226, -3.7059]","-3.7473<br/>[-3.7481, -3.7304]","-3.7202<br/>[-3.7210, -3.7044]","-3.7209<br/>[-3.7216, -3.7051]","-3.7247<br/>[-3.7254, -3.7088]","-3.7222<br/>[-3.7229, -3.7063]","-3.7204<br/>[-3.7211, -3.7046]","-3.7220<br/>[-3.7228, -3.7061]","-3.7189<br/>[-3.7196, -3.7031]","-3.7188<br/>[-3.7195, -3.7029]","-3.7183<br/>[-3.7190, -3.7024]","-3.7203<br/>[-3.7210, -3.7044]","-3.7191<br/>[-3.7199, -3.7033]","-3.7189<br/>[-3.7197, -3.7031]","-3.7190<br/>[-3.7198, -3.7032]","-3.7189<br/>[-3.7197, -3.7031]","-3.7185<br/>[-3.7192, -3.7026]","-3.7179<br/>[-3.7186, -3.7021]","-3.7179<br/>[-3.7186, -3.7021]","-3.7192<br/>[-3.7199, -3.7033]","-3.7154<br/>[-3.7161, -3.6997]","-3.7158<br/>[-3.7165, -3.7000]","-3.7190<br/>[-3.7198, -3.7032]","-3.7173<br/>[-3.7181, -3.7016]","-3.7173<br/>[-3.7181, -3.7015]","-3.7189<br/>[-3.7196, -3.7031]","-3.7166<br/>[-3.7173, -3.7008]","-3.7145<br/>[-3.7152, -3.6988]","-3.7186<br/>[-3.7193, -3.7028]","-3.7166<br/>[-3.7173, -3.7009]","-3.7156<br/>[-3.7163, -3.6999]","-3.7151<br/>[-3.7159, -3.6994]","-3.7156<br/>[-3.7163, -3.6999]","-3.7173<br/>[-3.7181, -3.7015]","-3.7183<br/>[-3.7190, -3.7025]","-3.7162<br/>[-3.7170, -3.7005]","-3.7152<br/>[-3.7159, -3.6994]","-3.7150<br/>[-3.7157, -3.6993]","-3.7158<br/>[-3.7166, -3.7001]","-3.7160<br/>[-3.7167, -3.7002]","-3.7155<br/>[-3.7163, -3.6998]","-3.7156<br/>[-3.7163, -3.6998]","-3.7155<br/>[-3.7162, -3.6997]","-3.7167<br/>[-3.7174, -3.7009]","-3.7154<br/>[-3.7162, -3.6997]","-3.7146<br/>[-3.7154, -3.6989]","-3.7149<br/>[-3.7156, -3.6992]"],["-2.1748<br/>[-2.2050, -2.1539]","-2.5274<br/>[-2.5454, -2.4894]","-3.2446<br/>[-3.3415, -3.1435]","-2.7222<br/>[-2.7393, -2.7079]","-2.8948<br/>[-3.0373, -2.7846]","-2.9636<br/>[-3.1228, -2.8479]","-2.9648<br/>[-3.2059, -2.8305]","-3.0904<br/>[-3.2657, -2.9673]","-3.1941<br/>[-3.3506, -3.0660]","-3.2285<br/>[-3.3656, -3.0973]","-3.1908<br/>[-3.3792, -3.0280]","-3.2695<br/>[-3.3944, -3.1563]","-3.3341<br/>[-3.4450, -3.2223]","-3.3442<br/>[-3.4668, -3.2087]","-3.3750<br/>[-3.4728, -3.2567]","-3.1914<br/>[-3.3913, -3.0179]","-3.3770<br/>[-3.4782, -3.2581]","-3.3872<br/>[-3.4848, -3.2715]","-3.4063<br/>[-3.5144, -3.2837]","-3.4492<br/>[-3.5652, -3.3019]","-3.4692<br/>[-3.6555, -3.2728]","-3.4907<br/>[-3.5857, -3.3602]","-3.4819<br/>[-3.7013, -3.3346]","-3.4901<br/>[-3.5673, -3.3880]","-3.5049<br/>[-3.5982, -3.3743]","-3.6179<br/>[-3.7657, -3.4370]","-3.6178<br/>[-3.7623, -3.4349]","-3.5220<br/>[-3.6158, -3.3895]","-3.6526<br/>[-3.8520, -3.4000]","-3.5324<br/>[-3.6255, -3.4029]","-3.5527<br/>[-3.6395, -3.4300]","-3.7320<br/>[-3.9171, -3.4963]","-3.5823<br/>[-3.6699, -3.4587]","-3.6064<br/>[-3.7102, -3.4560]","-3.6119<br/>[-3.7200, -3.4691]","-3.6488<br/>[-3.7466, -3.5042]","-3.4184<br/>[-3.5840, -3.2285]","-3.8024<br/>[-3.9878, -3.5662]","-3.6692<br/>[-3.7589, -3.5317]","-3.6671<br/>[-3.7581, -3.5308]","-3.9106<br/>[-4.0946, -3.6699]","-3.8265<br/>[-3.9945, -3.5879]","-3.6988<br/>[-3.8371, -3.5121]","-3.9606<br/>[-4.1278, -3.7383]","-3.8909<br/>[-4.0452, -3.6789]","-3.7220<br/>[-3.8036, -3.5918]","-3.8203<br/>[-3.9631, -3.6245]","-3.7697<br/>[-3.8758, -3.6171]","-3.9058<br/>[-4.0339, -3.7210]"]],"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":[["20","16","9","4","7","11","1","18","19","6","2","13","3","14","10","15","17","8","12","5"],[7632,9716,9058,11745,7741,9832,6985,6873,5539,8297,8395,7140,9525,8906,7839,7262,7941,9665,6804,10905],[21.9926221237335,11.7524804080877,9.29155703014007,3.81801166710491,3.07776152907557,1.94846759036667,1.5949200012806,0.520571602432786,0.264853535846885,0.0185285425273636,-0.0314638506956224,-0.168261585979361,-0.387312408270854,-0.493786624786828,-0.577788984114142,-0.679797201608212,-0.706400380593345,-0.837874088205992,-0.883514183836807,-0.883851489919066],["-3.7666<br/>[-3.7674, -3.7492]","-3.7280<br/>[-3.7288, -3.7119]","-3.7227<br/>[-3.7234, -3.7067]","-3.7267<br/>[-3.7274, -3.7106]","-3.7159<br/>[-3.7167, -3.7002]","-3.7191<br/>[-3.7199, -3.7033]","-3.7235<br/>[-3.7242, -3.7075]","-3.7203<br/>[-3.7210, -3.7045]","-3.7212<br/>[-3.7219, -3.7053]","-3.7212<br/>[-3.7219, -3.7053]","-3.7227<br/>[-3.7234, -3.7068]","-3.7194<br/>[-3.7202, -3.7036]","-3.7209<br/>[-3.7216, -3.7050]","-3.7207<br/>[-3.7215, -3.7048]","-3.7186<br/>[-3.7194, -3.7028]","-3.7168<br/>[-3.7175, -3.7010]","-3.7167<br/>[-3.7174, -3.7010]","-3.7178<br/>[-3.7186, -3.7021]","-3.7164<br/>[-3.7172, -3.7007]","-3.7155<br/>[-3.7162, -3.6998]"],["-2.2923<br/>[-2.2975, -2.2879]","-2.9533<br/>[-3.0684, -2.8740]","-3.0519<br/>[-3.1837, -2.9442]","-3.0861<br/>[-3.2008, -2.9901]","-3.2000<br/>[-3.3149, -3.0721]","-3.2256<br/>[-3.3742, -3.0913]","-2.8406<br/>[-2.9882, -2.7202]","-3.0014<br/>[-3.1625, -2.8786]","-3.0238<br/>[-3.1772, -2.8864]","-3.1185<br/>[-3.2928, -2.9731]","-3.1506<br/>[-3.3170, -3.0174]","-3.1703<br/>[-3.3395, -3.0165]","-3.2759<br/>[-3.4247, -3.1160]","-3.3303<br/>[-3.4544, -3.1833]","-3.3611<br/>[-3.5242, -3.1706]","-3.4394<br/>[-3.6148, -3.2395]","-3.4563<br/>[-3.6209, -3.2593]","-3.5616<br/>[-3.6969, -3.3845]","-3.7277<br/>[-3.9101, -3.4946]","-3.5899<br/>[-3.7020, -3.4318]"]],"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"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.4 plyr_1.8.4 dplyr_0.7.5 R.matlab_3.6.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 compiler_3.5.0 pillar_1.2.3
[4] later_0.7.3 git2r_0.21.0 workflowr_1.0.1
[7] bindr_0.1.1 R.methodsS3_1.7.1 R.utils_2.6.0
[10] tools_3.5.0 digest_0.6.15 jsonlite_1.5
[13] evaluate_0.10.1 tibble_1.4.2 pkgconfig_2.0.1
[16] rlang_0.2.1 shiny_1.1.0 crosstalk_1.0.0
[19] yaml_2.1.19 bindrcpp_0.2.2 stringr_1.3.1
[22] knitr_1.20 htmlwidgets_1.2 rprojroot_1.3-2
[25] tidyselect_0.2.4 glue_1.2.0 R6_2.2.2
[28] rmarkdown_1.10 purrr_0.2.5 magrittr_1.5
[31] whisker_0.3-2 backports_1.1.2 promises_1.0.1
[34] htmltools_0.3.6 assertthat_0.2.0 mime_0.5
[37] xtable_1.8-2 httpuv_1.4.4.1 stringi_1.2.3
[40] R.oo_1.22.0 </code></pre>
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