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<h1 class="title toc-ignore">Enrichment results of coronary artery disease</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/26343387">“A Comprehensive 1000 Genomes–based Genome-Wide Association Meta-Analysis of Coronary Artery Disease” (<em>Nature Genetics</em>, 2015)</a>. The summary data file is available at <a href="http://www.cardiogramplusc4d.org/data-downloads/" class="uri">http://www.cardiogramplusc4d.org/data-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>
<script type="application/json" data-for="htmlwidget-983860bb2d7d6ad3a872">{"x":{"filter":"none","data":[["acetate conversion to acetyl-CoA<br/>(158, biocyc, BioSystems)","Amino acid conjugation of benzoic acid<br/>(499, wiki, BioSystems)","LDL endocytosis<br/>(673, reactome, PC)","p75(NTR)-mediated signaling<br/>(3059, pid, BioSystems)","p75(NTR)-mediated signaling<br/>(3144, pid, PC)","NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria<br/>(1289, kegg, BioSystems)","Cyanoamino acid metabolism<br/>(894, kegg, BioSystems)","Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling<br/>(2778, pid, PC)","Platelet Amyloid Precursor Protein Pathway<br/>(1267, biocarta, BioCarta)","Glutathione synthesis and recycling<br/>(1226, reactome, PC)","Glutathione metabolism<br/>(2039, wiki, BioSystems)","Acute Myocardial Infarction<br/>(1721, biocarta, BioCarta)","Glutathione synthesis and recycling<br/>(1433, reactome, BioSystems)","Synthesis of Leukotrienes (LT) and Eoxins (EX)<br/>(1950, reactome, PC)","Aflatoxin activation and detoxification<br/>(1819, reactome, PC)","Lipoprotein metabolism<br/>(2378, reactome, PC)","Taurine and hypotaurine metabolism<br/>(1299, kegg, BioSystems)","Synthesis of Leukotrienes (LT) and Eoxins (EX)<br/>(2131, reactome, BioSystems)","Aflatoxin activation and detoxification<br/>(1966, reactome, BioSystems)","Adenosine P1 receptors<br/>(354, reactome, PC)","Glutathione conjugation<br/>(2465, reactome, PC)","Glutathione conjugation<br/>(2569, reactome, BioSystems)","Monoamine Transport<br/>(2452, wiki, BioSystems)","HIF-2-alpha transcription factor network<br/>(2466, pid, PC)","Vesicle-mediated transport<br/>(3831, reactome, BioSystems)","Glutathione metabolism<br/>(2956, kegg, BioSystems)","Activation of Matrix Metalloproteinases<br/>(2365, reactome, PC)","NGF-independant TRKA activation<br/>(557, reactome, PC)","Nucleotide GPCRs<br/>(1101, wiki, BioSystems)","Lipid and lipoprotein metabolism<br/>(2961, reactome, PC)","Arachidonic acid metabolism<br/>(2958, reactome, PC)","BDNF signaling pathway<br/>(3695, wiki, BioSystems)","Golgi Associated Vesicle Biogenesis<br/>(2932, reactome, PC)","Arachidonic acid metabolism<br/>(3023, reactome, BioSystems)","Clathrin derived vesicle budding<br/>(3067, reactome, PC)","Activation of TRKA receptors<br/>(652, reactome, PC)","Lipid digestion, mobilization, and transport<br/>(3093, reactome, BioSystems)","Syndecan-4-mediated signaling events<br/>(2455, pid, BioSystems)","Clathrin derived vesicle budding<br/>(3206, reactome, BioSystems)","Nucleotide-like (purinergic) receptors<br/>(1402, reactome, PC)","Lysosome<br/>(3629, kegg, BioSystems)","Arachidonic acid metabolism<br/>(3157, kegg, BioSystems)","Syndecan-4-mediated signaling events<br/>(2478, pid, PC)","Membrane Trafficking<br/>(3784, reactome, PC)","Membrane Trafficking<br/>(3795, reactome, BioSystems)","selenocysteine biosynthesis<br/>(722, humancyc, PC)","Angiopoietin receptor Tie2-mediated signaling<br/>(2879, pid, BioSystems)","Angiopoietin receptor Tie2-mediated signaling<br/>(2906, pid, PC)","Aminoacyl-tRNA...<br/>(2054, kegg, PC)","Phase II conjugation<br/>(3456, reactome, PC)","Cytosolic tRNA aminoacylation<br/>(2107, reactome, PC)","tRNA charging<br/>(2650, humancyc, PC)","Aminoacyl-tRNA biosynthesis, eukaryotes<br/>(2682, kegg, BioSystems)","Phase II conjugation<br/>(3482, reactome, BioSystems)","tRNA Aminoacylation<br/>(2782, reactome, PC)","Aminoacyl-tRNA biosynthesis<br/>(2843, kegg, BioSystems)","Neurotrophin signaling pathway<br/>(3622, kegg, BioSystems)","GPCRs, Other<br/>(3439, wiki, BioSystems)","Biological oxidations<br/>(3758, reactome, PC)","Biological oxidations<br/>(3767, reactome, BioSystems)","Fibrinolysis Pathway<br/>(1344, biocarta, BioCarta)","thymine degradation<br/>(280, humancyc, PC)","Wnt signaling pathway<br/>(3845, panther, PC)","Selenium Pathway<br/>(3432, wiki, BioSystems)","Wnt signaling pathway<br/>(3860, panther, PANTHER)","Cadherin signaling pathway<br/>(3714, panther, PC)","Dissolution of Fibrin Clot<br/>(1387, reactome, PC)","Cadherin signaling pathway<br/>(3675, panther, PANTHER)","Sm core complex<br/>(877, kegg, BioSystems)","Blood Clotting Cascade<br/>(1866, wiki, BioSystems)","Regulation of IGF Activity by IGFBP<br/>(1946, reactome, PC)","Post-Elongation Processing of Intronless pre-mRNA<br/>(2002, reactome, PC)","Spliceosome, U1-snRNP<br/>(1194, kegg, BioSystems)","Plasminogen activating cascade<br/>(1591, panther, PANTHER)","Plasminogen activating cascade<br/>(1638, panther, PC)","SLBP independent Processing of Histone Pre-mRNAs<br/>(1146, reactome, PC)","Chylomicron-mediated lipid transport<br/>(1698, reactome, PC)","Blood coagulation<br/>(2488, panther, PANTHER)","Staphylococcus aureus infection<br/>(3032, kegg, BioSystems)","TFs Regulate miRNAs related to cardiac hypertrophy<br/>(993, wiki, BioSystems)","Statin Pathway<br/>(2412, wiki, BioSystems)","Hemostasis<br/>(3914, reactome, PC)","SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs<br/>(1239, reactome, PC)","Blood coagulation<br/>(2636, panther, PC)","Hemostasis<br/>(3916, reactome, BioSystems)","Spliceosome, U4/U6.U5 tri-snRNP<br/>(2410, kegg, BioSystems)","Signaling by PDGF<br/>(3776, reactome, PC)","Platelet degranulation<br/>(3307, reactome, PC)","Spliceosome, U2-snRNP<br/>(1919, kegg, BioSystems)","amb2 Integrin signaling<br/>(2482, pid, PC)","Response to elevated platelet cytosolic Ca2+<br/>(3355, reactome, PC)","amb2 Integrin signaling<br/>(2926, pid, BioSystems)","Scavenging by Class A Receptors<br/>(1835, reactome, PC)","Methionine salvage pathway<br/>(1287, kegg, BioSystems)","C-MYB transcription factor network<br/>(3391, pid, PC)","Orphan transporters<br/>(3498, reactome, PC)","Complement and Coagulation Cascades<br/>(2953, wiki, BioSystems)","methionine salvage cycle III<br/>(1085, biocyc, BioSystems)","Degradation of the extracellular matrix<br/>(3442, reactome, PC)","Mitochondrial Carnitine Palmitoyltransferase (CPT) System<br/>(449, biocarta, BioCarta)"],[2,4,6,55,62,11,7,42,11,11,22,17,13,21,19,30,11,24,21,4,32,34,31,32,231,49,30,5,9,50,50,136,49,53,56,6,58,31,65,13,117,62,32,184,193,6,46,48,23,88,24,37,38,92,42,44,115,86,170,174,12,3,247,85,258,144,13,132,7,19,21,22,10,15,16,10,17,32,53,8,30,490,11,37,496,30,179,74,20,32,79,48,19,11,83,96,49,9,87,4],[242,258,557,5245,5818,840,492,4402,1420,844,1431,1564,956,1856,1281,2915,1113,1970,1393,440,2045,2157,3351,3008,22068,3373,2511,722,746,4433,4424,16051,5041,4538,5487,879,4990,3802,6425,981,10596,4930,3968,16758,17742,576,4801,5045,2098,6110,2104,3376,3475,6235,3941,4122,11969,9167,12196,12321,1184,740,28377,7922,29882,15366,1264,16599,602,1557,1837,1879,825,1251,1259,911,1281,2846,2571,689,2652,51341,971,3202,51734,2441,21589,7708,1674,2773,8617,4362,2523,940,8243,9706,4260,796,9586,367],[30.5260511438621,30.3034924928281,18.9216889990161,15.9818630770013,15.4158622935146,14.4597014633504,13.3557481040489,12.161630092972,11.9483468492885,11.9267804376743,11.7653390347403,11.7286152280499,11.7281055234927,11.4298501934408,11.4234650282457,11.3851188689214,11.3331743827611,11.3179827851775,11.2875915743971,11.2674483202353,10.8111452643774,10.7291554219715,10.6437970332664,10.5587339677484,10.5413886679316,10.1386186582258,10.1362983570406,9.95224443786138,9.92805779997095,9.8525951813869,9.65571423648019,9.58844831432923,9.58825934073015,9.54707662555277,9.46167600022818,9.45180949631068,9.31971731888691,9.30082091031001,9.27521294369805,9.17566138329276,9.15231259200385,9.11818728702395,9.07371267018342,8.84061615890985,8.79140057590069,8.72509797997018,8.66568896030587,8.36209163676557,8.35566992549866,8.26256771714444,8.19135766919638,8.12168743278863,8.10454148783436,8.08071487116326,8.04376349783638,8.01525360582704,7.97322319015939,7.95127621788546,7.94434029813098,7.82719757249906,7.77385820486071,7.62930447721979,7.62087206750818,7.59546782037184,7.57902758737724,7.53653508951718,7.5165688300606,7.48986933504565,7.43521328562072,7.14616438838284,7.05085874841695,6.93645788704174,6.45832334153976,6.00482193191232,6.0044667009873,5.90635075247036,5.82818309430762,5.82040315561443,5.53041706350967,5.50327617506547,5.43845917857112,5.34990925261949,5.34355366546104,5.33290757227326,5.31265167837492,5.20793221744997,4.92197864886288,4.87156117535455,4.33022588134742,4.16709588443632,4.03812291588183,4.00991180773639,3.97515505130496,3.92773875701408,3.89484481571364,3.86676344914897,3.71155501252449,3.31041672471678,3.18184948048248,-0.374115859076138],["-4.0938<br/>[-4.1500, 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-4.0301]","-4.0936<br/>[-4.1498, -4.0217]","-4.1036<br/>[-4.1607, -4.0305]","-4.1152<br/>[-4.1704, -4.0422]","-4.1032<br/>[-4.1603, -4.0301]","-4.0970<br/>[-4.1534, -4.0248]","-4.1013<br/>[-4.1553, -4.0300]","-4.0967<br/>[-4.1530, -4.0245]","-4.0939<br/>[-4.1501, -4.0219]","-4.1013<br/>[-4.1552, -4.0299]","-4.1014<br/>[-4.1553, -4.0301]","-4.0934<br/>[-4.1495, -4.0214]","-4.0939<br/>[-4.1501, -4.0219]","-4.1109<br/>[-4.1686, -4.0408]","-4.1109<br/>[-4.1686, -4.0408]","-4.0936<br/>[-4.1498, -4.0216]","-4.1126<br/>[-4.1707, -4.0384]","-4.1014<br/>[-4.1552, -4.0301]","-4.1009<br/>[-4.1548, -4.0296]","-4.1011<br/>[-4.1573, -4.0290]","-4.1179<br/>[-4.1763, -4.0431]","-4.1280<br/>[-4.1831, -4.0547]","-4.0936<br/>[-4.1498, -4.0216]","-4.1012<br/>[-4.1551, -4.0300]","-4.1279<br/>[-4.1830, -4.0546]","-4.0935<br/>[-4.1497, -4.0216]","-4.1178<br/>[-4.1717, -4.0461]","-4.1097<br/>[-4.1634, -4.0382]","-4.0977<br/>[-4.1537, -4.0259]","-4.1139<br/>[-4.1722, -4.0432]","-4.1094<br/>[-4.1631, -4.0379]","-4.1165<br/>[-4.1748, -4.0457]","-4.1105<br/>[-4.1681, -4.0368]","-4.0982<br/>[-4.1550, -4.0255]","-4.1024<br/>[-4.1594, -4.0296]","-4.1138<br/>[-4.1692, -4.0405]","-4.1005<br/>[-4.1544, -4.0293]","-4.0983<br/>[-4.1551, -4.0256]","-4.1061<br/>[-4.1597, -4.0348]","-4.0937<br/>[-4.1499, -4.0217]"],["-1.8381<br/>[-1.8902, -1.7804]","-1.9066<br/>[-1.9298, -1.8753]","-1.5398<br/>[-1.5403, -1.5336]","-2.6743<br/>[-2.6939, -2.6505]","-2.7146<br/>[-2.7288, -2.6829]","-2.5790<br/>[-2.6197, -2.5221]","-1.9476<br/>[-2.0337, -1.8826]","-2.4529<br/>[-2.4691, -2.4319]","-2.1646<br/>[-2.1859, -2.1544]","-2.2539<br/>[-2.3839, -2.1710]","-2.4025<br/>[-2.5274, -2.2712]","-2.2016<br/>[-2.2238, -2.1900]","-2.3098<br/>[-2.4350, -2.2178]","-2.5212<br/>[-2.6304, -2.4263]","-2.4256<br/>[-2.5587, -2.3384]","-2.2038<br/>[-2.3154, -2.1393]","-2.4125<br/>[-2.5196, -2.3307]","-2.5487<br/>[-2.6646, -2.4536]","-2.4639<br/>[-2.5992, -2.3730]","-1.9384<br/>[-1.9709, -1.8897]","-2.6321<br/>[-2.7394, -2.5387]","-2.6557<br/>[-2.7657, -2.5639]","-2.6392<br/>[-2.6666, -2.5939]","-2.5635<br/>[-2.6194, -2.4947]","-3.1362<br/>[-3.2859, -3.0660]","-2.8444<br/>[-2.9432, -2.7602]","-2.4024<br/>[-2.4245, -2.3819]","-2.1406<br/>[-2.1658, -2.0948]","-2.1556<br/>[-2.1773, -2.1195]","-2.4068<br/>[-2.4993, -2.3187]","-2.7957<br/>[-2.8340, -2.7221]","-3.2136<br/>[-3.3237, -3.1174]","-3.0176<br/>[-3.1181, -2.9324]","-2.8027<br/>[-2.8422, -2.7288]","-3.0554<br/>[-3.1576, -2.9678]","-2.2038<br/>[-2.2270, -2.1628]","-2.4720<br/>[-2.5440, -2.3810]","-2.5590<br/>[-2.5761, -2.5206]","-3.1175<br/>[-3.2269, -3.0290]","-2.2444<br/>[-2.2634, -2.2017]","-3.2109<br/>[-3.3639, -3.0983]","-2.8216<br/>[-2.8566, -2.7500]","-2.5766<br/>[-2.5929, -2.5532]","-3.3742<br/>[-3.4738, -3.2823]","-3.3894<br/>[-3.5050, -3.3021]","-2.7100<br/>[-2.7582, -2.6302]","-2.6078<br/>[-2.6217, -2.5795]","-2.6297<br/>[-2.6505, -2.5981]","-3.1010<br/>[-3.2662, -2.9533]","-2.8750<br/>[-2.8965, -2.8457]","-3.2364<br/>[-3.3096, -3.1213]","-3.3104<br/>[-3.4614, -3.1507]","-3.3254<br/>[-3.4770, -3.1726]","-2.8768<br/>[-2.8897, -2.8503]","-3.3777<br/>[-3.5239, -3.2152]","-3.4032<br/>[-3.5472, -3.2480]","-3.5295<br/>[-3.6648, -3.4014]","-3.4437<br/>[-3.5298, -3.3828]","-2.8145<br/>[-2.8253, -2.7950]","-2.8170<br/>[-2.8277, -2.7973]","-2.3643<br/>[-2.3889, -2.3337]","-2.3985<br/>[-2.4259, -2.3482]","-3.7342<br/>[-3.8564, -3.6304]","-2.6498<br/>[-2.7306, -2.6335]","-3.7537<br/>[-3.8641, -3.6437]","-3.7847<br/>[-3.9505, -3.6323]","-2.4106<br/>[-2.4312, -2.3814]","-3.8208<br/>[-3.9800, -3.6737]","-2.0325<br/>[-2.0576, -1.9905]","-2.4750<br/>[-2.4984, -2.4424]","-2.4895<br/>[-2.5152, -2.4509]","-2.7918<br/>[-2.8166, -2.7734]","-2.1306<br/>[-2.1530, -2.0958]","-2.2033<br/>[-2.2757, -2.1263]","-2.2072<br/>[-2.2894, -2.1377]","-2.2591<br/>[-2.2759, -2.2276]","-2.1414<br/>[-2.2573, -2.0686]","-2.6425<br/>[-2.6603, -2.6090]","-2.6810<br/>[-2.6969, -2.6519]","-2.0332<br/>[-2.1009, -1.9708]","-2.3431<br/>[-2.4825, -2.2213]","-3.4274<br/>[-3.5525, -3.3504]","-2.2582<br/>[-2.2780, -2.2290]","-2.6886<br/>[-2.7042, -2.6502]","-3.4320<br/>[-3.5461, -3.3529]","-2.4737<br/>[-2.4892, -2.4437]","-3.0925<br/>[-3.2613, -2.9971]","-2.8306<br/>[-3.0209, -2.7814]","-2.1902<br/>[-2.3898, -2.1547]","-2.4960<br/>[-2.5899, -2.4145]","-2.9189<br/>[-3.1185, -2.8303]","-2.6400<br/>[-2.7425, -2.5699]","-2.4419<br/>[-2.5623, -2.3648]","-2.3276<br/>[-2.4297, -2.2409]","-3.1113<br/>[-3.2864, -2.9965]","-3.0287<br/>[-3.1039, -2.8686]","-2.8243<br/>[-2.8286, -2.7627]","-2.3126<br/>[-2.4290, -2.1816]","-3.0396<br/>[-3.2169, -2.8580]","-3.2080<br/>[-4.1170, -2.7219]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(ID, 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":[["Adrenal Gland","Artery - Tibial","Artery - Aorta","Artery - Coronary","Prostate","Esophagus - Muscularis","Cells - Transformed fibroblasts","Pancreas","Liver","Colon - Sigmoid","Esophagus - Gastroesophageal Junction","Uterus","Cells - EBV-transformed lymphocytes","Lung","Ovary","Breast - Mammary Tissue","Skin - Not Sun Exposed (Suprapubic)","Pituitary","Vagina","Skin - Sun Exposed (Lower leg)","Brain - Caudate (basal ganglia)","Testis","Brain - Hippocampus","Brain - Hypothalamus","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Nerve - Tibial","Brain - Cerebellum","Brain - Frontal Cortex (BA9)","Brain - Anterior cingulate cortex (BA24)","Brain - Cortex","Brain - Nucleus accumbens (basal ganglia)","Thyroid","Heart - Atrial Appendage","Brain - Putamen (basal ganglia)","Muscle - Skeletal","Spleen","Small Intestine - Terminal Ileum","Colon - Transverse","Stomach","Esophagus - Mucosa","Heart - Left Ventricle","Whole Blood","Brain - Cerebellar Hemisphere"],[6077,6496,6817,6623,6086,6434,6585,5548,6802,6367,6264,6173,5470,5315,6401,6052,6318,6344,6255,6247,6947,6398,6165,6280,6044,6296,6118,6106,6610,6318,6282,6566,6656,6230,7033,6215,4336,5069,5728,5711,6021,6068,6237,6032],[1.25490478372302,0.572302325652414,0.554240727813292,0.470664323406963,0.181803192383821,0.0975920980418168,-0.103523952171238,-0.15622444086122,-0.234142851002791,-0.273765490689929,-0.282869049053532,-0.308048356899941,-0.314461707534535,-0.343155433653914,-0.345441528116037,-0.348667277057284,-0.350359459528366,-0.361324419116825,-0.375156990040807,-0.385767724754447,-0.388346113040662,-0.391428752742437,-0.404633238502471,-0.404663883287619,-0.406799477108466,-0.407641416210085,-0.412391993229907,-0.420713645562001,-0.431595314091834,-0.433196389406474,-0.437165297628749,-0.442337840410247,-0.452196865127699,-0.46466174823017,-0.477724381941506,-0.606095460683723,-0.606629567469044,-0.627815085774135,-0.650968337256542,-0.666795327823694,-0.682644573568706,-0.713947126631524,-0.730217707146899,-0.731165159404913],["-4.1065<br/>[-4.1641, -4.0328]","-4.0989<br/>[-4.1550, -4.0270]","-4.0990<br/>[-4.1550, -4.0271]","-4.0988<br/>[-4.1548, -4.0268]","-4.0978<br/>[-4.1545, -4.0252]","-4.0994<br/>[-4.1554, -4.0275]","-4.1000<br/>[-4.1567, -4.0273]","-4.0983<br/>[-4.1551, -4.0257]","-4.0961<br/>[-4.1524, -4.0239]","-4.0967<br/>[-4.1527, -4.0248]","-4.0966<br/>[-4.1527, -4.0248]","-4.0976<br/>[-4.1543, -4.0251]","-4.0975<br/>[-4.1543, -4.0249]","-4.0924<br/>[-4.1485, -4.0205]","-4.0975<br/>[-4.1542, -4.0249]","-4.0974<br/>[-4.1542, -4.0248]","-4.0973<br/>[-4.1541, -4.0247]","-4.0974<br/>[-4.1542, -4.0248]","-4.0973<br/>[-4.1541, -4.0247]","-4.0972<br/>[-4.1540, -4.0246]","-4.0957<br/>[-4.1521, -4.0235]","-4.0965<br/>[-4.1528, -4.0243]","-4.0959<br/>[-4.1522, -4.0237]","-4.0959<br/>[-4.1523, -4.0237]","-4.0925<br/>[-4.1486, -4.0206]","-4.0925<br/>[-4.1485, -4.0206]","-4.0925<br/>[-4.1485, -4.0206]","-4.0958<br/>[-4.1522, -4.0236]","-4.0959<br/>[-4.1523, -4.0237]","-4.0958<br/>[-4.1521, -4.0236]","-4.0958<br/>[-4.1521, -4.0235]","-4.0958<br/>[-4.1521, -4.0236]","-4.0923<br/>[-4.1484, -4.0204]","-4.0920<br/>[-4.1481, -4.0202]","-4.0957<br/>[-4.1520, -4.0235]","-4.0932<br/>[-4.1492, -4.0215]","-4.0929<br/>[-4.1491, -4.0210]","-4.0929<br/>[-4.1490, -4.0211]","-4.0927<br/>[-4.1488, -4.0209]","-4.0927<br/>[-4.1488, -4.0208]","-4.0926<br/>[-4.1486, -4.0207]","-4.0921<br/>[-4.1482, -4.0202]","-4.0920<br/>[-4.1481, -4.0202]","-4.0920<br/>[-4.1481, -4.0201]"],["-3.0428<br/>[-3.2548, -2.9404]","-3.1565<br/>[-3.3959, -3.0065]","-3.1664<br/>[-3.4176, -3.0152]","-3.1980<br/>[-3.4236, -3.0543]","-3.2999<br/>[-3.4604, -3.1679]","-3.2732<br/>[-3.6055, -3.0827]","-3.4315<br/>[-3.5850, -3.3058]","-3.4226<br/>[-3.6035, -3.2558]","-3.4339<br/>[-3.7686, -3.1512]","-3.4628<br/>[-3.7994, -3.2222]","-3.4721<br/>[-3.8001, -3.2352]","-3.5436<br/>[-3.6879, -3.3826]","-3.5563<br/>[-3.6669, -3.4192]","-3.5835<br/>[-3.6834, -3.4499]","-3.5784<br/>[-3.7116, -3.4284]","-3.5836<br/>[-3.7070, -3.4398]","-3.5841<br/>[-3.7112, -3.4384]","-3.5968<br/>[-3.7110, -3.4586]","-3.6103<br/>[-3.7203, -3.4762]","-3.6218<br/>[-3.7253, -3.4937]","-3.5832<br/>[-3.8295, -3.2651]","-3.6045<br/>[-3.8010, -3.4290]","-3.6043<br/>[-3.8497, -3.2728]","-3.6018<br/>[-3.8510, -3.2707]","-3.6300<br/>[-3.7903, -3.4722]","-3.6253<br/>[-3.7975, -3.4558]","-3.6353<br/>[-3.7951, -3.4773]","-3.6295<br/>[-3.8549, -3.2988]","-3.6342<br/>[-3.8609, -3.3011]","-3.6391<br/>[-3.8647, -3.3012]","-3.6466<br/>[-3.8655, -3.3101]","-3.6445<br/>[-3.8722, -3.3022]","-3.6733<br/>[-3.8289, -3.5184]","-3.6954<br/>[-3.8368, -3.5470]","-3.6801<br/>[-3.8958, -3.3262]","-3.8794<br/>[-4.2962, -3.6074]","-4.0887<br/>[-4.4914, -3.7688]","-4.0502<br/>[-4.4198, -3.7419]","-4.0469<br/>[-4.4109, -3.7410]","-4.1126<br/>[-4.4800, -3.8014]","-4.1379<br/>[-4.4862, -3.8405]","-4.2892<br/>[-4.7107, -3.9628]","-4.3596<br/>[-4.7623, -4.0252]","-4.4340<br/>[-4.8463, -4.0915]"]],"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":[["Heart_Atrial_Appendage","Liver","Stomach","Cells_Transformed_fibroblasts","Kidney_Cortex","Small_Intestine_Terminal_Ileum","Whole_Blood","Breast_Mammary_Tissue","Pancreas","Pituitary","Artery_Coronary","Adrenal_Gland","Prostate","Nerve_Tibial","Lung","Skin_Not_Sun_Exposed_(Suprapubic)","Skin_Sun_Exposed_(Lower_leg)","Testis","Minor_Salivary_Gland","Artery_Aorta","Artery_Tibial","Brain_Cerebellum","Thyroid","Brain_Cortex","Colon_Transverse","Muscle_Skeletal","Vagina","Colon_Sigmoid","Brain_Spinal_cord_(cervical_c-1)","Cells_EBV-transformed_lymphocytes","Brain_Caudate_(basal_ganglia)","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Esophagus_Mucosa","Spleen","Brain_Cerebellar_Hemisphere","Adipose_Visceral_(Omentum)","Adipose_Subcutaneous","Heart_Left_Ventricle","Brain_Hippocampus","Brain_Hypothalamus","Brain_Amygdala","Ovary","Uterus","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Frontal_Cortex_(BA9)","Brain_Substantia_nigra"],[11599,8822,9863,11375,9511,9320,7517,10366,8110,10042,12967,12987,9683,12997,8797,7249,7156,8477,8884,14914,13212,11334,12652,12547,8122,9175,7207,11303,13210,8255,12339,11957,12402,7287,7598,13989,10281,10557,11578,11573,12766,11824,12104,13015,14652,14808,13649,14229,13249],[7.8220447649034,5.43251840702812,0.405247828119571,0.211071956214633,-0.165430673369804,-0.228411954365812,-0.27614992128025,-0.336540957228142,-0.395855030432886,-0.404903273402879,-0.484811220609679,-0.492098697611957,-0.521953106126722,-0.569047479892587,-0.577523123729558,-0.583415765088489,-0.584333487590402,-0.595592061189708,-0.627519471014357,-0.629420431741844,-0.635972547579946,-0.656754638804321,-0.657345232735933,-0.665729848597592,-0.682324240567022,-0.687733069900009,-0.690034179918111,-0.707278876926263,-0.742419549889891,-0.746211017939096,-0.756501537759979,-0.761192477013076,-0.764837016518146,-0.771585385261814,-0.783106777582266,-0.797071039232481,-0.803989224450613,-0.822555300227612,-0.824549262823924,-0.891536654635884,-0.893917458262194,-0.896840283012004,-0.900434491942556,-0.91185203609505,-0.91228729078063,-0.916813509164196,-0.922621409302524,-0.926271130797752,-0.92681939038812],["-4.0966<br/>[-4.1532, -4.0243]","-4.1170<br/>[-4.1755, -4.0462]","-4.1014<br/>[-4.1583, -4.0285]","-4.1041<br/>[-4.1606, -4.0316]","-4.0963<br/>[-4.1529, -4.0238]","-4.0970<br/>[-4.1537, -4.0245]","-4.0943<br/>[-4.1504, -4.0224]","-4.0990<br/>[-4.1557, -4.0265]","-4.0971<br/>[-4.1536, -4.0247]","-4.0972<br/>[-4.1531, -4.0254]","-4.0956<br/>[-4.1514, -4.0240]","-4.0990<br/>[-4.1559, -4.0262]","-4.0959<br/>[-4.1526, -4.0234]","-4.0948<br/>[-4.1506, -4.0225]","-4.0912<br/>[-4.1473, -4.0194]","-4.0941<br/>[-4.1500, -4.0224]","-4.0941<br/>[-4.1500, -4.0224]","-4.0922<br/>[-4.1482, -4.0204]","-4.0939<br/>[-4.1499, -4.0222]","-4.0944<br/>[-4.1502, -4.0229]","-4.0955<br/>[-4.1514, -4.0239]","-4.0905<br/>[-4.1465, -4.0187]","-4.0911<br/>[-4.1470, -4.0194]","-4.0906<br/>[-4.1466, -4.0189]","-4.0922<br/>[-4.1482, -4.0204]","-4.0930<br/>[-4.1489, -4.0215]","-4.0918<br/>[-4.1479, -4.0199]","-4.0909<br/>[-4.1469, -4.0192]","-4.0900<br/>[-4.1460, -4.0183]","-4.0922<br/>[-4.1482, -4.0205]","-4.0935<br/>[-4.1495, -4.0218]","-4.0934<br/>[-4.1494, -4.0216]","-4.0934<br/>[-4.1494, -4.0216]","-4.0917<br/>[-4.1478, -4.0198]","-4.0916<br/>[-4.1477, -4.0198]","-4.0896<br/>[-4.1456, -4.0178]","-4.0921<br/>[-4.1481, -4.0203]","-4.0918<br/>[-4.1479, -4.0199]","-4.0915<br/>[-4.1475, -4.0199]","-4.0906<br/>[-4.1466, -4.0188]","-4.0908<br/>[-4.1467, -4.0191]","-4.0905<br/>[-4.1465, -4.0188]","-4.0901<br/>[-4.1462, -4.0183]","-4.0904<br/>[-4.1464, -4.0187]","-4.0908<br/>[-4.1467, -4.0192]","-4.0907<br/>[-4.1466, -4.0191]","-4.0903<br/>[-4.1463, -4.0186]","-4.0904<br/>[-4.1463, -4.0187]","-4.0903<br/>[-4.1463, -4.0186]"],["-3.7627<br/>[-3.9047, -3.6004]","-2.8171<br/>[-2.8770, -2.7624]","-3.3149<br/>[-3.4707, -3.1889]","-3.3773<br/>[-3.5548, -3.2493]","-3.5025<br/>[-3.6243, -3.3780]","-3.6125<br/>[-3.7973, -3.4303]","-3.5366<br/>[-3.6954, -3.4067]","-3.5927<br/>[-3.7307, -3.4702]","-3.6085<br/>[-3.7831, -3.4408]","-3.6089<br/>[-3.8321, -3.4330]","-3.6552<br/>[-3.9147, -3.4622]","-3.6983<br/>[-3.8072, -3.5820]","-3.7202<br/>[-3.8591, -3.5625]","-3.7254<br/>[-3.9564, -3.5281]","-3.8024<br/>[-3.8883, -3.6847]","-3.7980<br/>[-4.1075, -3.5484]","-3.8031<br/>[-4.1106, -3.5546]","-3.7837<br/>[-4.0992, -3.5336]","-3.8437<br/>[-4.0613, -3.6528]","-3.7666<br/>[-4.0053, -3.5713]","-3.7855<br/>[-4.0238, -3.5886]","-3.8400<br/>[-4.5304, -3.5577]","-3.8357<br/>[-3.9564, -3.6931]","-3.8250<br/>[-4.4585, -3.5429]","-3.9446<br/>[-4.3023, -3.6617]","-3.9139<br/>[-4.2986, -3.6519]","-4.0291<br/>[-4.3767, -3.7462]","-3.8949<br/>[-4.1726, -3.6628]","-3.9257<br/>[-4.5613, -3.6068]","-4.1180<br/>[-4.5074, -3.8296]","-3.9647<br/>[-4.1623, -3.7792]","-3.9848<br/>[-4.1792, -3.8005]","-3.9789<br/>[-4.1714, -3.7962]","-4.3967<br/>[-4.7777, -4.0927]","-4.4033<br/>[-4.7977, -4.0904]","-4.0084<br/>[-4.6304, -3.6670]","-4.1637<br/>[-4.4126, -3.9403]","-4.2096<br/>[-4.4455, -3.9963]","-4.1322<br/>[-4.4454, -3.8774]","-4.4158<br/>[-4.7428, -4.1495]","-4.2998<br/>[-4.5857, -4.0615]","-4.4136<br/>[-4.7382, -4.1482]","-4.3981<br/>[-4.7000, -4.1300]","-4.3567<br/>[-4.6682, -4.1014]","-4.2323<br/>[-4.5148, -3.9876]","-4.2388<br/>[-4.5195, -3.9947]","-4.3513<br/>[-4.6331, -4.1143]","-4.3190<br/>[-4.5898, -4.0926]","-4.4145<br/>[-4.7020, -4.1737]"]],"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":[["9","16","3","5","20","10","18","12","4","1","13","19","6","8","14","7","17","15","11","2"],[10113,10603,10670,12061,8619,8940,7770,7630,12854,7923,8130,6221,9434,10755,9880,8890,8880,8172,10907,9591],[8.54484664321069,3.10629780437979,1.56265187017548,1.09292011720488,-0.0104647704991931,-0.111236202015141,-0.240164357912052,-0.247537997746743,-0.252226645903778,-0.256535982080492,-0.334175536573426,-0.34251973578863,-0.484239628184912,-0.567602675223374,-0.614157630694898,-0.677792138937228,-0.697679593892184,-0.745545183915049,-0.755188190240434,-0.774489195989368],["-4.1011<br/>[-4.1584, -4.0279]","-4.1086<br/>[-4.1660, -4.0349]","-4.1107<br/>[-4.1677, -4.0377]","-4.1049<br/>[-4.1612, -4.0327]","-4.0968<br/>[-4.1531, -4.0249]","-4.1011<br/>[-4.1580, -4.0282]","-4.0933<br/>[-4.1494, -4.0215]","-4.0980<br/>[-4.1546, -4.0257]","-4.1010<br/>[-4.1579, -4.0283]","-4.0978<br/>[-4.1545, -4.0252]","-4.0958<br/>[-4.1517, -4.0240]","-4.0925<br/>[-4.1485, -4.0207]","-4.0947<br/>[-4.1505, -4.0231]","-4.0950<br/>[-4.1508, -4.0233]","-4.0914<br/>[-4.1474, -4.0196]","-4.0925<br/>[-4.1485, -4.0209]","-4.0924<br/>[-4.1484, -4.0206]","-4.0916<br/>[-4.1477, -4.0198]","-4.0917<br/>[-4.1477, -4.0200]","-4.0914<br/>[-4.1474, -4.0196]"],["-3.4222<br/>[-3.5195, -3.3196]","-3.0288<br/>[-3.1146, -2.9490]","-3.0830<br/>[-3.2869, -2.9473]","-3.1722<br/>[-3.3786, -3.0253]","-3.3480<br/>[-3.7189, -3.1215]","-3.4837<br/>[-3.6297, -3.3596]","-3.5139<br/>[-3.6984, -3.3243]","-3.5221<br/>[-3.7098, -3.3380]","-3.5672<br/>[-3.7184, -3.4098]","-3.5340<br/>[-3.7153, -3.3649]","-3.5521<br/>[-3.8499, -3.3100]","-3.6009<br/>[-3.7637, -3.4368]","-3.6754<br/>[-4.0145, -3.4222]","-3.7736<br/>[-4.0319, -3.5469]","-3.8527<br/>[-4.1112, -3.6357]","-4.0066<br/>[-4.3524, -3.7361]","-4.0573<br/>[-4.3543, -3.7899]","-4.3317<br/>[-4.6972, -4.0408]","-4.1038<br/>[-4.3691, -3.8422]","-4.2841<br/>[-4.6184, -4.0188]"]],"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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