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<h1 class="title toc-ignore">Enrichment results of waist-to-hip ratio</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/25673412">“New Genetic Loci Link Adipose and Insulin Biology to Body Fat Distribution” (<em>Nature</em>, 2015)</a>. The summary data file is available at <a href="https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files" class="uri">https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files</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":[["Signalling to ERK5<br/>(62, reactome, PC)","Translesion synthesis by POLK<br/>(1736, reactome, BioSystems)","2-oxoglutarate decarboxylation to succinyl-CoA<br/>(335, biocyc, BioSystems)","Trafficking of dietary sterols<br/>(250, reactome, PC)","Acetylation<br/>(6, reactome, PC)","MAPK (ERK5) signaling<br/>(468, kegg, BioSystems)","Caffeine metabolism<br/>(648, kegg, BioSystems)","TCA cycle<br/>(858, panther, PANTHER)","TCA cycle<br/>(940, panther, PC)","NGF signalling via TRKA from the plasma membrane<br/>(3804, reactome, PC)","Trk receptor signaling mediated by the MAPK pathway<br/>(2319, pid, BioSystems)","Lysine degradation, lysine => saccharopine => acetoacetyl-CoA<br/>(1291, kegg, BioSystems)","Trk receptor signaling mediated by the MAPK pathway<br/>(2526, pid, PC)","Tryptophan metabolism<br/>(2212, kegg, PC)","Mitochondrial tRNA aminoacylation<br/>(1941, reactome, PC)","Aminoacyl-tRNA biosynthesis, eukaryotes<br/>(2682, kegg, BioSystems)","Aminoacyl-tRNA...<br/>(2054, kegg, PC)","Focal Adhesion<br/>(3774, wiki, BioSystems)","MAPK signaling pathway<br/>(3844, kegg, BioSystems)","tRNA charging<br/>(2650, humancyc, PC)","Gap junction<br/>(3451, kegg, BioSystems)","Aminoacyl-tRNA biosynthesis<br/>(2843, kegg, BioSystems)","tRNA Aminoacylation<br/>(2782, reactome, PC)","MicroRNAs in cardiomyocyte hypertrophy<br/>(3421, wiki, BioSystems)","Integrin-mediated cell adhesion<br/>(3505, wiki, BioSystems)","Lysine catabolism<br/>(921, reactome, PC)","Arylamine metabolism<br/>(888, wiki, BioSystems)","Termination of translesion DNA synthesis<br/>(2401, reactome, BioSystems)","Signaling Pathways in Glioblastoma<br/>(3348, wiki, BioSystems)","Recycling of eIF2:GDP<br/>(814, reactome, PC)","TNF-alpha/NF-kB Signaling Pathway<br/>(3781, wiki, BioSystems)","BDNF signaling pathway<br/>(3695, wiki, BioSystems)","MAPKinase Signaling Pathway<br/>(3412, biocarta, 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Cohesion<br/>(3500, reactome, BioSystems)","Fanconi anemia pathway<br/>(2991, kegg, BioSystems)","Deposition of new CENPA-containing nucleosomes at the centromere<br/>(3245, reactome, BioSystems)","RHO GTPases Activate Formins<br/>(3612, reactome, BioSystems)","Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met)<br/>(3288, pid, BioSystems)","Chromosome Maintenance<br/>(3548, reactome, BioSystems)","Mitotic Prometaphase<br/>(3552, reactome, PC)","Uridine monophosphate biosynthesis, glutamine (+ PRPP) => UMP<br/>(315, kegg, BioSystems)","Resolution of Sister Chromatid Cohesion<br/>(3491, reactome, PC)","De novo pyrimidine ribonucleotides biosythesis<br/>(907, panther, PC)","De novo pyrimidine ribonucleotides biosythesis<br/>(972, panther, PANTHER)","Pyrimidine biosynthesis<br/>(693, reactome, PC)","Synthesis of glycosylphosphatidylinositol (GPI)<br/>(1573, reactome, PC)","Glycosylphosphatidyl...<br/>(1764, kegg, PC)","Retrograde neurotrophin signalling<br/>(1408, reactome, PC)","Post-translational modification<br/>(2116, reactome, PC)","Recycling pathway of L1<br/>(1945, reactome, PC)","Recycling pathway of L1<br/>(2027, reactome, BioSystems)","Glycosylphosphatidylinositol(GPI)-anchor biosynthesis<br/>(2141, kegg, BioSystems)","Synaptic vesicle cycle<br/>(3132, kegg, BioSystems)","Synaptic Vesicle Pathway<br/>(2951, wiki, BioSystems)","Endocrine and other factor-regulated calcium reabsorption<br/>(2873, kegg, BioSystems)","MHC class II antigen presentation<br/>(3514, reactome, PC)","Bacterial invasion of epithelial cells<br/>(3329, kegg, BioSystems)","Toll Like Receptor 4 (TLR4) Cascade<br/>(3596, reactome, BioSystems)","Toll-Like Receptors Cascades<br/>(3653, reactome, BioSystems)","Toll Like Receptor 4 (TLR4) Cascade<br/>(3625, reactome, PC)","Toll-Like Receptors Cascades<br/>(3674, reactome, PC)","L1CAM interactions<br/>(3454, reactome, PC)","L1CAM interactions<br/>(3460, reactome, BioSystems)","Cycling of Ran in nucleocytoplasmic transport<br/>(601, biocarta, BioCarta)","Circadian clock system<br/>(1009, panther, PC)","EGFR1 Signaling Pathway<br/>(3757, wiki, BioSystems)","Assembly of the RAD51-ssDNA nucleoprotein complex<br/>(520, reactome, PC)","The IPAF inflammasome<br/>(71, reactome, PC)","Regulation of cytoskeletal remodeling and cell spreading by IPP complex components<br/>(815, reactome, PC)","Regulation of cytoskeletal remodeling and cell spreading by IPP complex components<br/>(974, reactome, BioSystems)","The AIM2 inflammasome<br/>(244, reactome, PC)","Cation-coupled Chloride cotransporters<br/>(792, reactome, PC)","TNF signaling<br/>(703, reactome, PC)","Interleukin-1 processing<br/>(805, reactome, PC)","Proteolysis and Signaling Pathway of Notch <br/>(740, biocarta, BioCarta)","Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant<br/>(796, reactome, PC)","p38 signaling mediated by MAPKAP kinases<br/>(1924, pid, BioSystems)","Processing of Intronless Pre-mRNAs<br/>(1405, reactome, PC)","Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate<br/>(1537, kegg, BioSystems)","superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)<br/>(1339, humancyc, PC)","Activation of BID and translocation to mitochondria<br/>(348, reactome, PC)","Presynaptic phase of homologous DNA pairing and strand exchange<br/>(692, reactome, PC)","IL 18 Signaling Pathway<br/>(734, biocarta, BioCarta)","Homologous DNA pairing and strand exchange<br/>(803, reactome, PC)","Calcium signaling in the CD4+ TCR pathway<br/>(2269, pid, BioSystems)"],[2,17,3,3,2,4,5,7,8,202,28,11,33,26,21,38,23,177,246,37,87,44,42,84,96,8,7,30,78,7,181,136,84,157,115,155,37,273,344,100,6,103,159,104,10,45,13,79,96,51,68,112,71,101,102,3,94,8,8,6,15,18,13,24,21,22,24,61,49,46,98,76,109,126,116,132,88,89,5,9,169,5,2,7,8,3,7,6,7,6,7,20,13,14,12,4,6,6,7,27],[77,1421,263,129,202,217,428,466,553,21029,2333,798,2704,2410,1848,2924,1668,18245,22999,2830,10235,3468,3313,8764,9389,956,533,2264,6818,414,13709,13946,6577,14211,10223,18116,2809,28983,33015,8862,508,9072,13618,7970,599,3349,1834,6721,7409,3789,2499,8767,5955,5100,7868,206,7307,529,529,520,1110,1375,1388,1816,2537,2606,1850,5743,5493,5507,6563,8542,9402,10512,10004,11039,11187,11256,318,723,14944,484,139,1056,1056,163,465,306,447,465,548,1390,1004,1258,669,329,590,475,693,2320],[75.1591625012002,67.3460713090182,66.049014039369,63.9188210301002,62.0586500003385,59.281355558609,58.379070840131,56.0015857581576,55.1870086729711,53.4500410917602,53.1010966303027,52.9893422044294,52.0636838037053,52.0260057881973,50.451571697723,50.402804544095,50.319302674247,49.2218664896263,49.2159450119942,48.6504901218713,47.7103979253462,44.9276579924457,44.5509074792583,44.4723490267126,42.7406170032729,42.6717735851364,41.4091610226543,40.9365839919361,40.2854475004338,37.3886182217624,36.908159625807,36.7912335898047,35.4283798545273,34.8699234805544,32.0169128095378,31.820876587983,30.2339707029843,30.0101562109476,29.0527895885398,28.5650155103267,28.2012624459052,28.1676617711216,27.6395012947409,26.5872447413862,22.7408793807788,21.7831232433405,21.6896533821845,21.4706755677758,20.290493045707,20.2687145061161,20.0015229202136,19.9540916618582,19.5804650685423,19.5374164870386,19.3940721527732,19.0794488444037,18.8205383817749,18.5975143368225,18.5975143368225,18.3069442475713,17.5884809888005,17.3694006747623,17.2989827323969,17.1947129727457,17.1692428967967,17.1536620506077,17.1304425223863,16.5524559954709,16.5092391613835,16.4805688392469,16.3850758117674,16.3808583373266,16.3485400487303,16.3165382293292,16.297127045108,16.274860895068,16.2391048986968,16.2366107966244,16.119745855702,14.7199904953698,13.9294605001306,13.0196026980538,12.3466540226123,12.2494182797384,12.2494182797384,12.2123649285211,12.1577988089689,11.8105634514918,11.6671131818602,11.2030657825157,11.1926742363715,10.8542583165568,10.7713849712423,10.6086430936721,10.1174706174507,9.55572915956216,8.24113860542454,6.78578654601162,-0.844473026438009,-1.12858896454981],["-3.2827<br/>[-3.3125, -3.2827]","-3.2744<br/>[-3.3062, -3.2744]","-3.2753<br/>[-3.3072, -3.2753]","-3.2745<br/>[-3.3063, -3.2745]","-3.2744<br/>[-3.3063, -3.2744]","-3.2828<br/>[-3.3127, -3.2828]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2856<br/>[-3.3157, -3.2856]","-3.2841<br/>[-3.3140, -3.2841]","-3.2746<br/>[-3.3064, -3.2746]","-3.2840<br/>[-3.3140, -3.2840]","-3.2759<br/>[-3.3079, -3.2759]","-3.2754<br/>[-3.3074, -3.2754]","-3.2753<br/>[-3.3072, -3.2753]","-3.2754<br/>[-3.3073, -3.2754]","-3.2854<br/>[-3.3154, -3.2854]","-3.2855<br/>[-3.3154, -3.2855]","-3.2753<br/>[-3.3073, -3.2753]","-3.2837<br/>[-3.3136, -3.2837]","-3.2753<br/>[-3.3073, -3.2753]","-3.2753<br/>[-3.3072, -3.2753]","-3.2828<br/>[-3.3127, -3.2828]","-3.2851<br/>[-3.3151, -3.2851]","-3.2752<br/>[-3.3071, -3.2752]","-3.2745<br/>[-3.3064, -3.2745]","-3.2744<br/>[-3.3063, -3.2744]","-3.2832<br/>[-3.3130, -3.2832]","-3.2745<br/>[-3.3063, -3.2745]","-3.2846<br/>[-3.3145, 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-3.2754]","-3.2754<br/>[-3.3073, -3.2754]","-3.2753<br/>[-3.3072, -3.2753]","-3.2754<br/>[-3.3073, -3.2754]","-3.2760<br/>[-3.3079, -3.2760]","-3.2760<br/>[-3.3080, -3.2760]","-3.2753<br/>[-3.3072, -3.2753]","-3.2755<br/>[-3.3075, -3.2755]","-3.2753<br/>[-3.3072, -3.2753]","-3.2753<br/>[-3.3072, -3.2753]","-3.2752<br/>[-3.3071, -3.2752]","-3.2759<br/>[-3.3078, -3.2759]","-3.2765<br/>[-3.3086, -3.2765]","-3.2764<br/>[-3.3084, -3.2764]","-3.2764<br/>[-3.3085, -3.2764]","-3.2763<br/>[-3.3084, -3.2763]","-3.2765<br/>[-3.3086, -3.2765]","-3.2765<br/>[-3.3086, -3.2765]","-3.2744<br/>[-3.3063, -3.2744]","-3.2747<br/>[-3.3065, -3.2747]","-3.2870<br/>[-3.3170, -3.2870]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2750<br/>[-3.3069, -3.2750]","-3.2745<br/>[-3.3063, -3.2745]","-3.2750<br/>[-3.3069, -3.2750]","-3.2750<br/>[-3.3068, -3.2750]","-3.2754<br/>[-3.3073, -3.2754]","-3.2751<br/>[-3.3070, -3.2751]","-3.2753<br/>[-3.3072, -3.2753]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2745<br/>[-3.3063, -3.2745]","-3.2744<br/>[-3.3063, -3.2744]","-3.2743<br/>[-3.3061, -3.2743]"],["-0.4279<br/>[-0.4314, -0.4208]","-1.5911<br/>[-1.5920, -1.5789]","-1.1669<br/>[-1.1828, -1.1399]","-0.9376<br/>[-0.9924, -0.8810]","-1.0704<br/>[-1.0808, -1.0342]","-0.9979<br/>[-1.0933, -0.8914]","-1.4637<br/>[-1.4842, -1.4262]","-1.5396<br/>[-1.6070, -1.4959]","-1.5827<br/>[-1.6476, -1.5377]","-2.5208<br/>[-2.5208, -2.5096]","-1.9479<br/>[-1.9683, -1.9431]","-1.6718<br/>[-1.6852, -1.6441]","-1.9845<br/>[-1.9908, -1.9813]","-2.1484<br/>[-2.1492, -2.1484]","-2.1652<br/>[-2.2361, -2.1607]","-2.1300<br/>[-2.1300, -2.1286]","-2.1206<br/>[-2.2388, -1.9814]","-2.8860<br/>[-2.8860, -2.8860]","-2.9441<br/>[-2.9441, -2.9441]","-2.1244<br/>[-2.1394, -2.0364]","-2.6011<br/>[-2.6011, -2.5988]","-2.0469<br/>[-2.0470, -2.0462]","-2.0968<br/>[-2.0976, -2.0962]","-2.6359<br/>[-2.6374, -2.6359]","-2.4222<br/>[-2.4237, -2.4222]","-1.5010<br/>[-1.5039, -1.4862]","-1.2156<br/>[-1.2200, -1.2140]","-1.5580<br/>[-1.5585, -1.5510]","-2.6488<br/>[-2.6488, -2.6486]","-1.3094<br/>[-1.3208, -1.3045]","-2.5314<br/>[-2.5365, -2.5314]","-2.5313<br/>[-2.5338, -2.5313]","-2.3954<br/>[-2.4092, -2.3768]","-2.6853<br/>[-2.6876, -2.6825]","-2.5575<br/>[-2.5635, -2.5178]","-2.7445<br/>[-2.7464, -2.7445]","-1.5838<br/>[-1.5841, -1.5814]","-2.9589<br/>[-2.9703, -2.9408]","-2.9808<br/>[-2.9808, -2.9785]","-2.3616<br/>[-2.3683, -2.3375]","-1.7412<br/>[-1.8725, -1.6177]","-2.3709<br/>[-2.3771, -2.3669]","-2.7811<br/>[-2.7848, -2.7805]","-2.7857<br/>[-2.7881, -2.7831]","-2.2689<br/>[-2.4202, -2.1128]","-1.6419<br/>[-1.6419, -1.6360]","-1.9932<br/>[-1.9933, -1.9932]","-2.8621<br/>[-2.8622, -2.8612]","-2.7800<br/>[-2.7833, -2.7800]","-1.6176<br/>[-1.6176, -1.6176]","-2.7059<br/>[-2.8325, -2.5597]","-2.7450<br/>[-2.7468, -2.7450]","-2.9027<br/>[-2.9818, -2.7919]","-2.9347<br/>[-3.0152, -2.8194]","-2.7506<br/>[-2.7513, -2.7506]","-1.8933<br/>[-2.0013, -1.7745]","-2.9187<br/>[-2.9628, -2.8449]","-2.1748<br/>[-2.3619, -2.0117]","-2.1748<br/>[-2.3619, -2.0117]","-2.1947<br/>[-2.2857, -2.0740]","-2.3869<br/>[-2.5962, -2.2090]","-2.4970<br/>[-2.6763, -2.3258]","-2.5324<br/>[-2.6964, -2.3596]","-2.5895<br/>[-2.7572, -2.4146]","-2.6348<br/>[-2.7733, -2.4891]","-2.6413<br/>[-2.7801, -2.4964]","-2.6242<br/>[-2.7745, -2.4574]","-2.9063<br/>[-2.9934, -2.7814]","-2.9359<br/>[-3.0207, -2.8088]","-2.9556<br/>[-3.0363, -2.8377]","-2.9967<br/>[-3.0710, -2.8819]","-2.9652<br/>[-3.0331, -2.8656]","-2.9745<br/>[-3.0322, -2.8816]","-2.9793<br/>[-3.0338, -2.8941]","-2.9961<br/>[-3.0493, -2.9086]","-2.9962<br/>[-3.0471, -2.9118]","-3.0147<br/>[-3.0624, -2.9325]","-3.0153<br/>[-3.0629, -2.9389]","-2.0513<br/>[-2.1787, -1.9168]","-1.4844<br/>[-1.4879, -1.4741]","-2.7549<br/>[-2.7781, -2.7549]","-2.0332<br/>[-2.1750, -1.9063]","-1.6882<br/>[-1.8248, -1.5615]","-2.3921<br/>[-2.4682, -2.3294]","-2.3921<br/>[-2.4682, -2.3294]","-1.7487<br/>[-1.8958, -1.6085]","-1.4908<br/>[-1.4910, -1.4881]","-1.8599<br/>[-1.9847, -1.7446]","-2.0854<br/>[-2.2735, -1.9434]","-2.0190<br/>[-2.1559, -1.8372]","-2.0850<br/>[-2.2326, -1.9594]","-2.1408<br/>[-2.2203, -2.0760]","-2.2762<br/>[-2.4355, -2.1440]","-1.3175<br/>[-1.3191, -1.3175]","-1.4242<br/>[-1.4278, -1.4136]","-1.6650<br/>[-1.6901, -1.6151]","-1.7253<br/>[-1.7661, -1.6816]","-1.9055<br/>[-1.9058, -1.9055]","-3.0447<br/>[-3.3820, -2.6970]","-3.1125<br/>[-3.2804, -2.8885]"]],"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":[["Heart - Left Ventricle","Muscle - Skeletal","Spleen","Pituitary","Heart - Atrial Appendage","Testis","Breast - Mammary Tissue","Nerve - Tibial","Uterus","Pancreas","Adipose - Subcutaneous","Skin - Sun Exposed (Lower leg)","Cells - EBV-transformed lymphocytes","Liver","Adrenal Gland","Prostate","Small Intestine - Terminal Ileum","Cells - Transformed fibroblasts","Colon - Sigmoid","Esophagus - Gastroesophageal Junction","Skin - Not Sun Exposed (Suprapubic)","Adipose - Visceral (Omentum)","Ovary","Esophagus - Muscularis","Artery - Tibial","Artery - Coronary","Lung","Colon - Transverse","Stomach","Artery - Aorta","Vagina","Brain - Hypothalamus","Esophagus - Mucosa","Brain - Cerebellar Hemisphere","Brain - Hippocampus","Brain - Anterior cingulate cortex (BA24)","Brain - Cerebellum","Whole Blood","Thyroid","Brain - Nucleus accumbens (basal ganglia)","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)","Brain - Cortex","Brain - Frontal Cortex (BA9)"],[5018,5211,3722,5452,5249,5389,5139,5299,5257,4700,5273,5315,4571,5736,5088,5177,4337,5678,5469,5373,5379,5460,5480,5544,5629,5735,4692,4890,4923,5914,5394,5502,5281,5304,5400,5557,5317,5481,5780,5721,6028,6136,5496,5829],[-1.14378256937488,-1.15545971043116,-1.17171827829158,-1.17238730207835,-1.19277206846325,-1.19771756741598,-1.20156882342243,-1.20185417064783,-1.22448226074192,-1.23151443415525,-1.23343951207172,-1.23576740823989,-1.25024694525739,-1.26228313175355,-1.26419353813646,-1.27040235417383,-1.2817198656429,-1.29407382997401,-1.30915264991009,-1.30970592248308,-1.31132676578362,-1.31791139133385,-1.3188876852545,-1.32162742741818,-1.32194473824231,-1.3264476657803,-1.33860601516651,-1.34819700519141,-1.3503379288344,-1.35659353504393,-1.38296967135492,-1.39062734869067,-1.39660849713278,-1.40097753673261,-1.40648981466243,-1.41266019382836,-1.41272064606951,-1.42263939979327,-1.42435918779428,-1.42986593574631,-1.45715471551715,-1.46858139575573,-1.76224030951909,-1.7870653372146],["-3.2755<br/>[-3.3075, -3.2755]","-3.2756<br/>[-3.3075, -3.2756]","-3.2745<br/>[-3.3064, -3.2745]","-3.2753<br/>[-3.3072, -3.2753]","-3.2755<br/>[-3.3074, -3.2755]","-3.2754<br/>[-3.3073, -3.2754]","-3.2752<br/>[-3.3071, -3.2752]","-3.2754<br/>[-3.3073, -3.2754]","-3.2752<br/>[-3.3071, -3.2752]","-3.2747<br/>[-3.3065, -3.2747]","-3.2753<br/>[-3.3072, -3.2753]","-3.2747<br/>[-3.3066, -3.2747]","-3.2747<br/>[-3.3066, -3.2747]","-3.2750<br/>[-3.3069, -3.2750]","-3.2746<br/>[-3.3065, -3.2746]","-3.2751<br/>[-3.3070, -3.2751]","-3.2746<br/>[-3.3064, -3.2746]","-3.2752<br/>[-3.3071, -3.2752]","-3.2750<br/>[-3.3069, -3.2750]","-3.2749<br/>[-3.3068, -3.2749]","-3.2747<br/>[-3.3066, -3.2747]","-3.2749<br/>[-3.3067, -3.2749]","-3.2747<br/>[-3.3065, -3.2747]","-3.2749<br/>[-3.3068, -3.2749]","-3.2750<br/>[-3.3069, -3.2750]","-3.2750<br/>[-3.3069, -3.2750]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2749<br/>[-3.3068, -3.2749]","-3.2744<br/>[-3.3063, -3.2744]","-3.2744<br/>[-3.3063, -3.2744]","-3.2743<br/>[-3.3061, -3.2743]","-3.2743<br/>[-3.3061, -3.2743]","-3.2741<br/>[-3.3060, -3.2741]","-3.2742<br/>[-3.3060, -3.2742]","-3.2742<br/>[-3.3060, -3.2742]","-3.2742<br/>[-3.3061, -3.2742]","-3.2743<br/>[-3.3061, -3.2743]","-3.2742<br/>[-3.3060, -3.2742]","-3.2741<br/>[-3.3060, -3.2741]","-3.2741<br/>[-3.3059, -3.2741]","-3.2749<br/>[-3.3068, -3.2749]","-3.2749<br/>[-3.3068, -3.2749]"],["-2.9461<br/>[-3.0627, -2.7901]","-2.9502<br/>[-3.0633, -2.7918]","-3.0464<br/>[-3.1706, -2.8705]","-2.9580<br/>[-3.0647, -2.8116]","-2.9778<br/>[-3.0844, -2.8253]","-2.9800<br/>[-3.0773, -2.8401]","-2.9840<br/>[-3.1172, -2.8046]","-2.9811<br/>[-3.0962, -2.8186]","-3.0030<br/>[-3.1207, -2.8419]","-3.0286<br/>[-3.1502, -2.8591]","-3.0094<br/>[-3.1168, -2.8564]","-3.0096<br/>[-3.1310, -2.8415]","-3.0508<br/>[-3.1725, -2.8768]","-3.0216<br/>[-3.1120, -2.8877]","-3.0456<br/>[-3.1516, -2.8907]","-3.0483<br/>[-3.1510, -2.8933]","-3.1106<br/>[-3.2245, -2.9422]","-3.0505<br/>[-3.1461, -2.9078]","-3.0751<br/>[-3.1701, -2.9278]","-3.0806<br/>[-3.1753, -2.9336]","-3.0811<br/>[-3.1952, -2.9182]","-3.0830<br/>[-3.1854, -2.9245]","-3.0841<br/>[-3.1972, -2.9184]","-3.0850<br/>[-3.1776, -2.9433]","-3.0811<br/>[-3.1735, -2.9391]","-3.0807<br/>[-3.1726, -2.9373]","-3.1622<br/>[-3.2660, -3.0029]","-3.1598<br/>[-3.2596, -3.0092]","-3.1599<br/>[-3.2607, -3.0072]","-3.1052<br/>[-3.1927, -2.9708]","-3.1705<br/>[-3.2639, -3.0197]","-3.1735<br/>[-3.2654, -3.0299]","-3.2012<br/>[-3.2933, -3.0549]","-3.2063<br/>[-3.2971, -3.0593]","-3.2064<br/>[-3.3003, -3.0515]","-3.2029<br/>[-3.2926, -3.0612]","-3.2248<br/>[-3.3158, -3.0818]","-3.2266<br/>[-3.3148, -3.0825]","-3.2032<br/>[-3.2908, -3.0586]","-3.2173<br/>[-3.3035, -3.0812]","-3.2370<br/>[-3.3189, -3.1035]","-3.2476<br/>[-3.3274, -3.1119]","-3.1180<br/>[-3.2149, -2.9702]","-3.1293<br/>[-3.2210, -2.9849]"]],"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","Adipose_Subcutaneous","Adipose_Visceral_(Omentum)","Vagina","Esophagus_Mucosa","Breast_Mammary_Tissue","Testis","Liver","Skin_Not_Sun_Exposed_(Suprapubic)","Skin_Sun_Exposed_(Lower_leg)","Spleen","Cells_Transformed_fibroblasts","Muscle_Skeletal","Artery_Tibial","Pancreas","Stomach","Whole_Blood","Lung","Cells_EBV-transformed_lymphocytes","Minor_Salivary_Gland","Heart_Left_Ventricle","Prostate","Pituitary","Kidney_Cortex","Colon_Transverse","Ovary","Uterus","Small_Intestine_Terminal_Ileum","Adrenal_Gland","Brain_Cerebellum","Nerve_Tibial","Artery_Coronary","Brain_Hippocampus","Brain_Putamen_(basal_ganglia)","Brain_Amygdala","Esophagus_Gastroesophageal_Junction","Brain_Caudate_(basal_ganglia)","Colon_Sigmoid","Brain_Nucleus_accumbens_(basal_ganglia)","Esophagus_Muscularis","Brain_Cortex","Brain_Hypothalamus","Brain_Spinal_cord_(cervical_c-1)","Brain_Anterior_cingulate_cortex_(BA24)","Thyroid","Brain_Substantia_nigra","Artery_Aorta","Brain_Cerebellar_Hemisphere","Brain_Frontal_Cortex_(BA9)"],[10110,9254,9104,6498,6564,9183,7051,7235,6590,6529,6770,10162,8077,11840,7050,8696,6738,7994,7375,8006,10056,8513,9003,8230,7107,10937,11669,8238,11243,10315,11755,11704,10344,10719,10582,12902,10621,10410,10707,13055,11258,11514,12083,12227,11434,12070,13529,12893,12910],[16.3368987571157,0.218608560262209,-0.950050684784317,-1.26601355507589,-1.31922614427277,-1.37406911541463,-1.38665180421492,-1.39770187162707,-1.4066233860819,-1.40710299740252,-1.41645672524935,-1.42584239356467,-1.44580968436317,-1.45061453097111,-1.45153243114115,-1.45609031319122,-1.45831222870682,-1.46535463624045,-1.50914309761829,-1.51233435170747,-1.51272849732173,-1.51374917248479,-1.52382375910061,-1.5312700415358,-1.53843820541548,-1.58889199910362,-1.59124731224726,-1.59918491653563,-1.60441319953399,-1.61613347153298,-1.64075246400826,-1.64441770557484,-1.64669050012893,-1.64993324494066,-1.65086904943256,-1.65121300238432,-1.66078695360446,-1.66291863834115,-1.66389399509518,-1.6751621227732,-1.69756334981621,-1.70093954126236,-1.70298666558718,-1.7071463536011,-1.71687421605586,-1.72000620273411,-1.72560326434885,-1.73295624269649,-1.73711501924886],["-3.2766<br/>[-3.3086, -3.2766]","-3.2819<br/>[-3.3143, -3.2819]","-3.2788<br/>[-3.3109, -3.2788]","-3.2758<br/>[-3.3077, -3.2758]","-3.2753<br/>[-3.3073, -3.2753]","-3.2761<br/>[-3.3081, -3.2761]","-3.2749<br/>[-3.3068, -3.2749]","-3.2747<br/>[-3.3066, -3.2747]","-3.2749<br/>[-3.3068, -3.2749]","-3.2749<br/>[-3.3068, -3.2749]","-3.2749<br/>[-3.3068, -3.2749]","-3.2757<br/>[-3.3077, -3.2757]","-3.2752<br/>[-3.3071, -3.2752]","-3.2764<br/>[-3.3085, -3.2764]","-3.2743<br/>[-3.3061, -3.2743]","-3.2753<br/>[-3.3073, -3.2753]","-3.2744<br/>[-3.3063, -3.2744]","-3.2751<br/>[-3.3070, -3.2751]","-3.2743<br/>[-3.3061, -3.2743]","-3.2745<br/>[-3.3064, -3.2745]","-3.2753<br/>[-3.3072, -3.2753]","-3.2748<br/>[-3.3067, -3.2748]","-3.2745<br/>[-3.3064, -3.2745]","-3.2740<br/>[-3.3058, -3.2740]","-3.2738<br/>[-3.3057, -3.2738]","-3.2748<br/>[-3.3067, -3.2748]","-3.2754<br/>[-3.3074, -3.2754]","-3.2736<br/>[-3.3055, -3.2736]","-3.2739<br/>[-3.3058, -3.2739]","-3.2742<br/>[-3.3061, -3.2742]","-3.2744<br/>[-3.3063, -3.2744]","-3.2740<br/>[-3.3059, -3.2740]","-3.2738<br/>[-3.3057, -3.2738]","-3.2740<br/>[-3.3058, -3.2740]","-3.2739<br/>[-3.3057, -3.2739]","-3.2750<br/>[-3.3070, -3.2750]","-3.2737<br/>[-3.3056, -3.2737]","-3.2737<br/>[-3.3055, -3.2737]","-3.2737<br/>[-3.3056, -3.2737]","-3.2749<br/>[-3.3068, -3.2749]","-3.2734<br/>[-3.3053, -3.2734]","-3.2734<br/>[-3.3052, -3.2734]","-3.2738<br/>[-3.3056, -3.2738]","-3.2737<br/>[-3.3056, -3.2737]","-3.2733<br/>[-3.3051, -3.2733]","-3.2735<br/>[-3.3053, -3.2735]","-3.2740<br/>[-3.3059, -3.2740]","-3.2736<br/>[-3.3055, -3.2736]","-3.2735<br/>[-3.3053, -3.2735]"],["-2.9693<br/>[-3.0302, -2.8773]","-2.6122<br/>[-2.7655, -2.4947]","-2.8374<br/>[-2.9316, -2.7243]","-3.0067<br/>[-3.0778, -2.9000]","-3.0448<br/>[-3.1214, -2.9247]","-3.0251<br/>[-3.0934, -2.9150]","-3.0898<br/>[-3.1593, -2.9782]","-3.0933<br/>[-3.1670, -2.9736]","-3.1309<br/>[-3.1990, -3.0218]","-3.1346<br/>[-3.2021, -3.0261]","-3.1324<br/>[-3.2078, -3.0127]","-3.0468<br/>[-3.0973, -2.9626]","-3.1113<br/>[-3.1771, -2.9992]","-3.0379<br/>[-3.0856, -2.9564]","-3.1600<br/>[-3.2372, -3.0341]","-3.1025<br/>[-3.1626, -3.0013]","-3.1871<br/>[-3.2634, -3.0594]","-3.1356<br/>[-3.1976, -3.0295]","-3.2220<br/>[-3.2895, -3.1037]","-3.1911<br/>[-3.2562, -3.0834]","-3.1167<br/>[-3.1725, -3.0190]","-3.1698<br/>[-3.2305, -3.0671]","-3.1619<br/>[-3.2224, -3.0555]","-3.2055<br/>[-3.2667, -3.0961]","-3.2926<br/>[-3.3606, -3.1716]","-3.1697<br/>[-3.2198, -3.0815]","-3.1510<br/>[-3.1933, -3.0718]","-3.3190<br/>[-3.3775, -3.2168]","-3.2034<br/>[-3.2594, -3.1031]","-3.2259<br/>[-3.2796, -3.1305]","-3.2044<br/>[-3.2512, -3.1228]","-3.2109<br/>[-3.2560, -3.1305]","-3.2710<br/>[-3.3206, -3.1838]","-3.2578<br/>[-3.3070, -3.1702]","-3.2658<br/>[-3.3149, -3.1782]","-3.1819<br/>[-3.2194, -3.1101]","-3.2800<br/>[-3.3287, -3.1899]","-3.2951<br/>[-3.3443, -3.2035]","-3.2809<br/>[-3.3288, -3.1910]","-3.2054<br/>[-3.2408, -3.1388]","-3.3112<br/>[-3.3559, -3.2251]","-3.3039<br/>[-3.3476, -3.2184]","-3.2803<br/>[-3.3237, -3.1947]","-3.2808<br/>[-3.3234, -3.2045]","-3.3385<br/>[-3.3824, -3.2574]","-3.3102<br/>[-3.3521, -3.2313]","-3.2584<br/>[-3.2977, -3.1820]","-3.2948<br/>[-3.3353, -3.2144]","-3.3012<br/>[-3.3412, -3.2204]"]],"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":[["13","20","1","18","19","10","3","9","12","8","2","6","11","7","14","16","17","15","5","4"],[6990,7224,6859,6680,5246,7512,8997,8746,6787,9601,8275,8189,9708,7725,8586,9505,7868,7326,10603,11521],[-0.694456260760395,-0.780694744454424,-0.806191426667087,-0.828587896152864,-0.884121291135656,-0.926554303424788,-0.937337287424889,-0.949160743064856,-0.960730121525771,-0.987800948447391,-0.988828198331288,-1.01676584886037,-1.01848359885137,-1.02307543904672,-1.02665327392139,-1.039793210125,-1.04385027473304,-1.0691241381916,-1.12787026107443,-1.17338905238634],["-3.2764<br/>[-3.3084, -3.2764]","-3.2756<br/>[-3.3076, -3.2756]","-3.2756<br/>[-3.3075, -3.2756]","-3.2753<br/>[-3.3072, -3.2753]","-3.2744<br/>[-3.3062, -3.2744]","-3.2747<br/>[-3.3066, -3.2747]","-3.2757<br/>[-3.3077, -3.2757]","-3.2756<br/>[-3.3076, -3.2756]","-3.2743<br/>[-3.3061, -3.2743]","-3.2759<br/>[-3.3079, -3.2759]","-3.2749<br/>[-3.3068, -3.2749]","-3.2741<br/>[-3.3060, -3.2741]","-3.2754<br/>[-3.3074, -3.2754]","-3.2744<br/>[-3.3063, -3.2744]","-3.2745<br/>[-3.3063, -3.2745]","-3.2744<br/>[-3.3063, -3.2744]","-3.2743<br/>[-3.3062, -3.2743]","-3.2739<br/>[-3.3058, -3.2739]","-3.2740<br/>[-3.3059, -3.2740]","-3.2743<br/>[-3.3062, -3.2743]"],["-2.9343<br/>[-3.0195, -2.8133]","-2.9806<br/>[-3.0648, -2.8580]","-3.0039<br/>[-3.0916, -2.8703]","-3.0244<br/>[-3.1166, -2.8883]","-3.1468<br/>[-3.2431, -2.9956]","-3.0867<br/>[-3.1583, -2.9679]","-3.0556<br/>[-3.1249, -2.9412]","-3.0724<br/>[-3.1345, -2.9709]","-3.1535<br/>[-3.2299, -3.0262]","-3.0845<br/>[-3.1387, -2.9953]","-3.1209<br/>[-3.1928, -3.0044]","-3.1558<br/>[-3.2228, -3.0446]","-3.1083<br/>[-3.1636, -3.0170]","-3.1867<br/>[-3.2625, -3.0621]","-3.1506<br/>[-3.2209, -3.0296]","-3.1336<br/>[-3.1930, -3.0314]","-3.2061<br/>[-3.2725, -3.0946]","-3.2836<br/>[-3.3501, -3.1720]","-3.1964<br/>[-3.2466, -3.1043]","-3.2212<br/>[-3.2686, -3.1368]"]],"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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