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<h1 class="title toc-ignore">Enrichment results of age at natural menopause</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/26414677">“Large-Scale Genomic Analyses Link Reproductive Aging to Hypothalamic Signaling, Breast Cancer Susceptibility and <em>BRCA1</em>-Mediated Dna Repair” (<em>Nature Genetics</em>, 2015)</a>. The summary data file is available at <a href="http://www.reprogen.org/data_download.html" class="uri">http://www.reprogen.org/data_download.html</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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wall<br/>(reactome, PC)","Triacylglycerol biosynthesis<br/>(kegg, BioSystems)","Constitutive PI3K/AKT Signaling in Cancer<br/>(reactome, PC)","Validated targets of C-MYC transcriptional repression<br/>(pid, BioSystems)","Gap junction assembly<br/>(reactome, PC)","Amphetamine addiction<br/>(kegg, BioSystems)","Signaling events regulated by Ret tyrosine kinase<br/>(pid, BioSystems)","Insulin receptor signalling cascade<br/>(reactome, BioSystems)","IRS-related events triggered by IGF1R<br/>(reactome, BioSystems)","Energy dependent regulation of mTOR by LKB1-AMPK<br/>(reactome, BioSystems)","noradrenaline and adrenaline degradation<br/>(humancyc, PC)","MicroRNAs in cancer<br/>(kegg, BioSystems)","IRS-mediated signalling<br/>(reactome, BioSystems)","SHC1 events in ERBB2 signaling<br/>(reactome, PC)","Signaling by Insulin receptor<br/>(reactome, BioSystems)","E2F transcription factor network<br/>(pid, BioSystems)","Bladder cancer<br/>(kegg, BioSystems)","Dopamine receptor mediated signaling pathway<br/>(panther, PANTHER)","a6b1 and a6b4 Integrin signaling<br/>(pid, BioSystems)","ErbB4 signaling events<br/>(pid, PC)","ErbB receptor signaling network<br/>(pid, PC)","Pancreatic cancer<br/>(kegg, BioSystems)","Endometrial cancer<br/>(kegg, BioSystems)","PLCG1 events in ERBB2 signaling<br/>(reactome, BioSystems)","Non-small cell lung cancer<br/>(kegg, BioSystems)","SUMOylation<br/>(reactome, BioSystems)","Stress Induction of HSP Regulation<br/>(biocarta, BioCarta)","Ion transport by P-type ATPases<br/>(reactome, BioSystems)"],[37,5,53,2,4,77,65,13,3,5,8,13,15,47,13,17,50,24,22,27,64,26,27,32,58,57,50,112,14,5,48,35,63,18,45,30,41,30,37,33,33,23,21,25,47,36,51,133,132,71,136,134,121,130,132,123,67,3,150,84,284,288,190,128,72,21,78,27,29,93,38,39,98,17,84,62,18,64,38,271,271,27,9,149,268,32,292,69,37,43,31,35,15,63,50,37,55,76,15,43],[3100,504,5291,239,432,6441,5797,1266,356,343,607,1457,1528,5002,1750,1994,4778,2161,2246,2341,5951,2870,2955,4788,4881,5501,4031,8974,1017,811,4620,2744,5799,1958,4869,4258,3730,2576,3202,2749,2689,2316,2104,2693,4581,5667,5140,7722,7634,5766,9083,8993,8237,8725,8815,8327,5203,400,10607,6874,18970,19170,17469,11272,3596,1742,7474,1908,2098,8773,3193,3286,8667,1544,8979,5546,1072,7680,3911,25574,25606,2523,815,15112,25162,4356,27242,5512,3354,4159,2867,6167,3004,5849,6088,5757,7247,6199,1123,4862],[866.69505872936,830.119092946871,809.426335488375,800.311737779352,795.061619810762,650.11660946176,645.571223492253,542.706613060823,540.935884808782,540.93065433068,540.50726908708,539.723191077576,539.683340589206,539.60962649335,539.599794860379,539.456494907337,539.451076661773,539.415947898208,539.34795210329,539.344624521568,539.199912758907,539.129069296256,539.123210899928,538.947890298153,538.926371320275,532.353693130073,516.742829043057,497.885912027261,427.162938956823,144.327801585349,143.250810280226,142.984476086054,142.687507696241,142.652618665748,142.314412148359,142.310301481672,142.168201402501,140.039648634076,139.932507503002,139.840971018953,138.900902129825,138.589089296672,137.982787537389,137.657601618195,90.7605788658795,90.1585827433641,43.5833227892156,27.2544952578789,27.2543560762856,26.4926075648446,25.6723044489924,25.4761965177845,25.1166115125766,25.078650089716,25.0781502846626,25.0769039355639,24.6931553572952,23.4745513313902,23.0816614699456,17.6316979989177,15.4298490854167,15.4219604440771,9.90217308437028,5.20537646438753,5.144995370017,3.72390326312919,3.43119112285188,3.09980214970365,3.09645597210102,2.9594891507606,2.90017500981764,2.89967157162649,2.86816545819951,2.76440571786171,2.70910593575796,2.18908399693338,2.10713326445418,1.9205710142722,1.85255061128303,1.58258887976593,1.58238314550286,1.55679536858664,1.54564742456165,1.52638587755031,1.51455961309985,1.41096559618717,1.38105657222168,1.29326906986103,1.29046658905591,1.24693148382325,1.19325819649948,1.18882640765755,1.1842820330537,0.920548689307421,0.893875402794307,0.871952097439635,0.836586827513447,0.708265766946011,0.0360370503630286,-0.0228245219685918],["-4.2298<br/>[-4.2412, -4.2298]","-4.2309<br/>[-4.2423, -4.2309]","-4.2293<br/>[-4.2407, -4.2293]","-4.2310<br/>[-4.2424, -4.2310]","-4.2309<br/>[-4.2423, -4.2309]","-4.2361<br/>[-4.2478, -4.2361]","-4.2364<br/>[-4.2481, -4.2364]","-4.2377<br/>[-4.2493, -4.2377]","-4.2309<br/>[-4.2423, -4.2309]","-4.2309<br/>[-4.2423, -4.2309]","-4.2308<br/>[-4.2422, -4.2308]","-4.2305<br/>[-4.2419, -4.2305]","-4.2304<br/>[-4.2418, -4.2304]","-4.2361<br/>[-4.2477, -4.2361]","-4.2303<br/>[-4.2417, -4.2303]","-4.2302<br/>[-4.2416, -4.2302]","-4.2291<br/>[-4.2405, -4.2291]","-4.2302<br/>[-4.2416, -4.2302]","-4.2301<br/>[-4.2415, -4.2301]","-4.2301<br/>[-4.2415, -4.2301]","-4.2286<br/>[-4.2400, -4.2286]","-4.2299<br/>[-4.2413, -4.2299]","-4.2298<br/>[-4.2412, -4.2298]","-4.2295<br/>[-4.2409, -4.2295]","-4.2294<br/>[-4.2408, -4.2294]","-4.2366<br/>[-4.2482, -4.2366]","-4.2298<br/>[-4.2412, -4.2298]","-4.2539<br/>[-4.2658, -4.2539]","-4.2450<br/>[-4.2568, -4.2450]","-4.2307<br/>[-4.2421, -4.2307]","-4.2325<br/>[-4.2438, -4.2325]","-4.2301<br/>[-4.2415, -4.2301]","-4.2354<br/>[-4.2470, -4.2354]","-4.2302<br/>[-4.2416, -4.2302]","-4.2290<br/>[-4.2404, -4.2290]","-4.2293<br/>[-4.2407, -4.2293]","-4.2297<br/>[-4.2411, -4.2297]","-4.2300<br/>[-4.2414, -4.2300]","-4.2297<br/>[-4.2411, -4.2297]","-4.2299<br/>[-4.2413, -4.2299]","-4.2300<br/>[-4.2414, -4.2300]","-4.2301<br/>[-4.2415, -4.2301]","-4.2302<br/>[-4.2416, -4.2302]","-4.2299<br/>[-4.2414, -4.2299]","-4.2292<br/>[-4.2406, -4.2292]","-4.2287<br/>[-4.2401, -4.2287]","-4.2294<br/>[-4.2408, -4.2294]","-4.2496<br/>[-4.2616, -4.2496]","-4.2497<br/>[-4.2616, -4.2497]","-4.2358<br/>[-4.2474, -4.2358]","-4.2417<br/>[-4.2535, -4.2417]","-4.2417<br/>[-4.2535, -4.2417]","-4.2421<br/>[-4.2538, -4.2421]","-4.2419<br/>[-4.2536, -4.2419]","-4.2418<br/>[-4.2536, -4.2418]","-4.2420<br/>[-4.2538, -4.2420]","-4.2365<br/>[-4.2481, -4.2365]","-4.2312<br/>[-4.2427, -4.2312]","-4.2414<br/>[-4.2532, -4.2414]","-4.2432<br/>[-4.2550, -4.2432]","-4.2525<br/>[-4.2647, -4.2525]","-4.2524<br/>[-4.2646, -4.2524]","-4.2456<br/>[-4.2572, -4.2456]","-4.2368<br/>[-4.2483, -4.2368]","-4.2363<br/>[-4.2479, -4.2363]","-4.2381<br/>[-4.2497, -4.2381]","-4.2354<br/>[-4.2469, -4.2354]","-4.2358<br/>[-4.2472, -4.2358]","-4.2357<br/>[-4.2472, -4.2357]","-4.2352<br/>[-4.2467, -4.2352]","-4.2375<br/>[-4.2491, -4.2375]","-4.2374<br/>[-4.2491, -4.2374]","-4.2307<br/>[-4.2421, -4.2307]","-4.2525<br/>[-4.2645, -4.2525]","-4.2276<br/>[-4.2390, -4.2276]","-4.2355<br/>[-4.2471, -4.2355]","-4.2310<br/>[-4.2425, -4.2310]","-4.2350<br/>[-4.2466, -4.2350]","-4.2327<br/>[-4.2440, -4.2327]","-4.2351<br/>[-4.2468, -4.2351]","-4.2351<br/>[-4.2468, -4.2351]","-4.2306<br/>[-4.2421, -4.2306]","-4.2307<br/>[-4.2421, -4.2307]","-4.2318<br/>[-4.2434, -4.2318]","-4.2352<br/>[-4.2470, -4.2352]","-4.2293<br/>[-4.2407, -4.2293]","-4.2344<br/>[-4.2461, -4.2344]","-4.2288<br/>[-4.2402, -4.2288]","-4.2297<br/>[-4.2411, -4.2297]","-4.2293<br/>[-4.2407, -4.2293]","-4.2299<br/>[-4.2413, -4.2299]","-4.2289<br/>[-4.2403, -4.2289]","-4.2298<br/>[-4.2412, -4.2298]","-4.2287<br/>[-4.2401, -4.2287]","-4.2286<br/>[-4.2400, -4.2286]","-4.2287<br/>[-4.2401, -4.2287]","-4.2281<br/>[-4.2395, -4.2281]","-4.2356<br/>[-4.2472, -4.2356]","-4.2240<br/>[-4.2352, -4.2240]","-4.2224<br/>[-4.2336, -4.2224]"],["-2.4893<br/>[-2.4901, -2.4893]","-1.6559<br/>[-1.6559, -1.6559]","-2.5931<br/>[-2.5931, -2.5931]","-1.3605<br/>[-1.3605, -1.3604]","-1.6172<br/>[-1.6173, -1.6172]","-2.5938<br/>[-2.5938, -2.5938]","-2.5686<br/>[-2.5686, -2.5640]","-2.4959<br/>[-2.5019, -2.4899]","-2.2350<br/>[-2.2468, -2.2231]","-2.2331<br/>[-2.2342, -2.2314]","-2.4813<br/>[-2.4821, -2.4802]","-2.8614<br/>[-2.8624, -2.8599]","-2.8765<br/>[-2.8824, -2.8700]","-3.2190<br/>[-3.2215, -3.2160]","-2.9412<br/>[-2.9420, -2.9401]","-2.9978<br/>[-2.9986, -2.9966]","-3.2188<br/>[-3.2449, -3.2027]","-3.0310<br/>[-3.0335, -3.0277]","-3.0417<br/>[-3.0496, -3.0318]","-3.0659<br/>[-3.0681, -3.0626]","-3.3177<br/>[-3.3481, -3.2987]","-3.1561<br/>[-3.1568, -3.1551]","-3.1651<br/>[-3.1691, -3.1605]","-3.3022<br/>[-3.3640, -3.2470]","-3.3247<br/>[-3.3722, -3.2816]","-3.0991<br/>[-3.1236, -3.0750]","-2.6286<br/>[-2.6911, -2.5907]","-2.7826<br/>[-2.7925, -2.7664]","-1.8540<br/>[-1.8666, -1.8249]","-2.4191<br/>[-2.4276, -2.4112]","-2.9758<br/>[-3.0331, -2.9475]","-2.8905<br/>[-2.9176, -2.8745]","-3.1585<br/>[-3.1600, -3.1576]","-2.8109<br/>[-2.8131, -2.8093]","-3.1955<br/>[-3.2085, -3.1795]","-3.1159<br/>[-3.1358, -3.1017]","-3.0473<br/>[-3.0652, -3.0369]","-2.8046<br/>[-2.8084, -2.8024]","-2.8987<br/>[-2.9028, -2.8962]","-2.8337<br/>[-2.8373, -2.8317]","-2.9118<br/>[-2.9345, -2.8927]","-2.8735<br/>[-2.8799, -2.8693]","-2.8325<br/>[-2.8385, -2.8287]","-2.9413<br/>[-2.9469, -2.9379]","-3.1505<br/>[-3.1705, -3.1280]","-3.1600<br/>[-3.2412, -3.1208]","-2.9204<br/>[-2.9919, -2.8821]","-3.0350<br/>[-3.0901, -3.0314]","-3.0300<br/>[-3.0853, -3.0264]","-3.0330<br/>[-3.0514, -3.0243]","-3.2422<br/>[-3.2469, -3.2389]","-3.2397<br/>[-3.2430, -3.2368]","-3.2044<br/>[-3.2065, -3.2019]","-3.2299<br/>[-3.2312, -3.2265]","-3.2343<br/>[-3.2357, -3.2309]","-3.2099<br/>[-3.2112, -3.2066]","-3.0715<br/>[-3.0856, -3.0635]","-2.1252<br/>[-2.2758, -2.1244]","-3.3070<br/>[-3.3898, -3.2986]","-3.2298<br/>[-3.2298, -3.2298]","-3.4654<br/>[-3.4654, -3.4651]","-3.4699<br/>[-3.4699, -3.4696]","-3.2147<br/>[-3.2314, -3.2076]","-3.4337<br/>[-3.5627, -3.3180]","-2.9632<br/>[-2.9833, -2.9544]","-2.7289<br/>[-2.7398, -2.7233]","-3.2970<br/>[-3.3283, -3.2841]","-2.8070<br/>[-2.8122, -2.8043]","-2.8481<br/>[-2.8534, -2.8454]","-3.3706<br/>[-3.4440, -3.3400]","-3.0032<br/>[-3.0128, -2.9975]","-3.0156<br/>[-3.0252, -3.0100]","-3.5280<br/>[-3.6068, -3.4829]","-2.4891<br/>[-2.4895, -2.4887]","-3.4628<br/>[-3.5030, -3.4457]","-3.4389<br/>[-3.4441, -3.4356]","-2.7300<br/>[-2.7329, -2.7263]","-3.5749<br/>[-3.5825, -3.5700]","-3.2615<br/>[-3.3680, -3.2089]","-3.7912<br/>[-3.7979, -3.7879]","-3.7918<br/>[-3.7985, -3.7885]","-3.0801<br/>[-3.0985, -3.0645]","-2.9021<br/>[-2.9124, -2.8902]","-3.8342<br/>[-3.8617, -3.8188]","-3.7850<br/>[-3.7914, -3.7818]","-3.5328<br/>[-3.6270, -3.4505]","-3.8207<br/>[-3.8269, -3.8176]","-3.6518<br/>[-3.7231, -3.5946]","-3.4187<br/>[-3.5087, -3.3506]","-3.5906<br/>[-3.6189, -3.5645]","-3.4466<br/>[-3.4610, -3.4330]","-3.5828<br/>[-3.7192, -3.5163]","-3.4718<br/>[-3.4819, -3.4628]","-3.7191<br/>[-3.7662, -3.6812]","-3.7571<br/>[-3.7884, -3.7305]","-3.7567<br/>[-3.7691, -3.7486]","-3.8209<br/>[-3.8624, -3.7868]","-3.4687<br/>[-3.4798, -3.4628]","-3.6734<br/>[-5.2118, -3.1448]","-6.0666<br/>[-6.9151, -5.5872]"]],"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":[["Heart - Atrial Appendage","Muscle - Skeletal","Heart - Left Ventricle","Brain - Nucleus accumbens (basal ganglia)","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)","Brain - Hypothalamus","Testis","Spleen","Cells - EBV-transformed lymphocytes","Breast - Mammary Tissue","Uterus","Skin - Sun Exposed (Lower leg)","Skin - Not Sun Exposed (Suprapubic)","Prostate","Ovary","Cells - Transformed fibroblasts","Colon - Sigmoid","Whole Blood","Pituitary","Adrenal Gland","Liver","Brain - Cerebellar Hemisphere","Vagina","Nerve - Tibial","Esophagus - Mucosa","Brain - Cortex","Brain - Anterior cingulate cortex (BA24)","Brain - Frontal Cortex (BA9)","Brain - Cerebellum","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Pancreas","Small Intestine - Terminal Ileum","Lung","Colon - Transverse","Stomach","Brain - Hippocampus","Esophagus - Gastroesophageal Junction","Esophagus - Muscularis","Thyroid","Artery - Tibial","Artery - Coronary","Artery - Aorta"],[5783,5581,5580,6040,6402,6479,5838,5772,3983,4921,5504,5626,5663,5730,5529,5802,6045,5866,5779,5847,5581,6234,5561,5727,5620,5549,5740,5836,6110,5606,5547,5760,5066,4656,4961,5193,5219,5683,5761,5944,6108,5989,6105,6272],[707.451160562699,706.160081608142,706.15725041773,704.533788431883,704.424610367814,704.394713480278,451.323282012997,307.356003799115,258.486970341809,253.607197629839,229.048065368708,227.155346923128,227.111100419384,227.089587416052,226.98006886351,226.939657149503,226.915069926887,226.712978286083,174.512339292206,90.5374688600811,77.7876888263472,68.3831505621993,22.8739343425411,4.19334592733483,1.57457033052689,1.54302533222653,1.4353325617567,1.40399059864824,1.34601231345555,1.31971306212197,1.24502878295291,1.21472478084215,1.09901330313707,-0.405177370769208,-0.415391923039479,-0.419058518342172,-0.421496732358003,-0.429820314779035,-0.432987652024963,-0.435972025368228,-0.438094857606062,-0.438134462485074,-0.443525018413619,-0.445243254280317],["-4.2358<br/>[-4.2474, -4.2358]","-4.2288<br/>[-4.2402, -4.2288]","-4.2288<br/>[-4.2402, -4.2288]","-4.2286<br/>[-4.2400, -4.2286]","-4.2284<br/>[-4.2398, -4.2284]","-4.2284<br/>[-4.2398, -4.2284]","-4.2220<br/>[-4.2333, -4.2220]","-4.2291<br/>[-4.2405, -4.2291]","-4.2294<br/>[-4.2409, -4.2294]","-4.2291<br/>[-4.2405, -4.2291]","-4.2359<br/>[-4.2475, -4.2359]","-4.2288<br/>[-4.2402, -4.2288]","-4.2288<br/>[-4.2402, -4.2288]","-4.2287<br/>[-4.2401, -4.2287]","-4.2288<br/>[-4.2402, -4.2288]","-4.2287<br/>[-4.2401, -4.2287]","-4.2286<br/>[-4.2400, -4.2286]","-4.2287<br/>[-4.2401, -4.2287]","-4.2397<br/>[-4.2512, -4.2397]","-4.2323<br/>[-4.2437, -4.2323]","-4.2300<br/>[-4.2414, -4.2300]","-4.2219<br/>[-4.2331, -4.2219]","-4.2292<br/>[-4.2407, -4.2292]","-4.2291<br/>[-4.2405, -4.2291]","-4.2292<br/>[-4.2406, -4.2292]","-4.2222<br/>[-4.2334, -4.2222]","-4.2221<br/>[-4.2333, -4.2221]","-4.2220<br/>[-4.2333, -4.2220]","-4.2219<br/>[-4.2332, -4.2219]","-4.2221<br/>[-4.2334, -4.2221]","-4.2291<br/>[-4.2406, -4.2291]","-4.2291<br/>[-4.2405, -4.2291]","-4.2228<br/>[-4.2341, -4.2228]","-4.2225<br/>[-4.2338, -4.2225]","-4.2224<br/>[-4.2336, -4.2224]","-4.2223<br/>[-4.2335, -4.2223]","-4.2223<br/>[-4.2335, -4.2223]","-4.2221<br/>[-4.2333, -4.2221]","-4.2221<br/>[-4.2333, -4.2221]","-4.2220<br/>[-4.2332, -4.2220]","-4.2219<br/>[-4.2332, -4.2219]","-4.2220<br/>[-4.2332, -4.2220]","-4.2219<br/>[-4.2332, -4.2219]","-4.2218<br/>[-4.2331, -4.2218]"],["-2.8611<br/>[-2.8745, -2.8474]","-2.9072<br/>[-2.9289, -2.8922]","-2.9065<br/>[-2.9286, -2.8906]","-3.0739<br/>[-3.0795, -3.0689]","-3.0994<br/>[-3.1043, -3.0940]","-3.1047<br/>[-3.1100, -3.0998]","-3.2789<br/>[-3.2874, -3.2710]","-3.2626<br/>[-3.2731, -3.2399]","-2.8596<br/>[-2.8867, -2.8339]","-2.8952<br/>[-2.8973, -2.8896]","-3.0130<br/>[-3.0275, -2.9950]","-3.1207<br/>[-3.1372, -3.0998]","-3.1223<br/>[-3.1405, -3.1026]","-3.1299<br/>[-3.1453, -3.1082]","-3.1057<br/>[-3.1178, -3.0862]","-3.1294<br/>[-3.1418, -3.1099]","-3.1518<br/>[-3.1654, -3.1340]","-3.1301<br/>[-3.1401, -3.1141]","-3.0037<br/>[-3.1047, -2.9341]","-2.4812<br/>[-2.4812, -2.4806]","-2.6938<br/>[-2.6965, -2.6803]","-2.7131<br/>[-2.7148, -2.7043]","-2.8356<br/>[-2.8359, -2.8260]","-3.1561<br/>[-3.3298, -3.0303]","-3.3629<br/>[-3.7152, -3.1627]","-3.3789<br/>[-3.7277, -3.1947]","-3.3758<br/>[-3.7722, -3.1144]","-3.3996<br/>[-3.7576, -3.1262]","-3.4405<br/>[-3.7908, -3.1778]","-3.4592<br/>[-3.7562, -3.2268]","-3.5370<br/>[-3.7378, -3.3562]","-3.5618<br/>[-3.7549, -3.3852]","-3.0692<br/>[-3.7557, -2.9110]","-4.4892<br/>[-5.7914, -3.8509]","-4.5484<br/>[-5.8207, -3.9010]","-4.5532<br/>[-5.8322, -3.9159]","-4.5748<br/>[-5.8395, -3.9305]","-4.5982<br/>[-5.8648, -3.9508]","-4.6210<br/>[-5.8738, -3.9866]","-4.6285<br/>[-5.8822, -3.9852]","-4.6375<br/>[-5.8843, -3.9871]","-4.6482<br/>[-5.8880, -3.9975]","-4.6900<br/>[-5.9051, -4.0467]","-4.6880<br/>[-5.9090, -4.0390]"]],"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_Left_Ventricle","Brain_Cortex","Heart_Atrial_Appendage","Spleen","Brain_Hippocampus","Brain_Amygdala","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Frontal_Cortex_(BA9)","Brain_Cerebellum","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Cerebellar_Hemisphere","Pituitary","Cells_EBV-transformed_lymphocytes","Brain_Hypothalamus","Testis","Cells_Transformed_fibroblasts","Lung","Whole_Blood","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis","Vagina","Skin_Sun_Exposed_(Lower_leg)","Esophagus_Mucosa","Skin_Not_Sun_Exposed_(Suprapubic)","Breast_Mammary_Tissue","Muscle_Skeletal","Artery_Coronary","Adrenal_Gland","Pancreas","Adipose_Visceral_(Omentum)","Colon_Sigmoid","Ovary","Uterus","Small_Intestine_Terminal_Ileum","Adipose_Subcutaneous","Brain_Substantia_nigra","Brain_Spinal_cord_(cervical_c-1)","Brain_Nucleus_accumbens_(basal_ganglia)","Colon_Transverse","Liver","Nerve_Tibial","Minor_Salivary_Gland","Prostate","Stomach","Kidney_Cortex","Thyroid","Artery_Tibial","Artery_Aorta"],[10832,11730,10931,6978,10709,10972,12712,13389,10689,11458,11556,13270,9333,7643,11969,7567,10523,8140,6995,13819,13992,6640,6673,6711,6748,9659,8475,12127,11985,7530,9620,10714,11335,12189,8528,9928,12444,12418,11117,7362,8038,12212,8210,8939,9063,8821,11764,12345,14019],[1009.74452034185,779.488142275085,608.932134943689,567.729822972998,539.024076882486,538.960056565778,538.775975327914,538.706342581554,538.528280055444,538.236281175065,538.209399616344,537.715709245301,509.639377168404,446.226825915242,334.555966398993,270.203472939618,240.789433643554,174.698289250641,170.190682797756,118.808405509597,117.830068134469,114.627761000018,112.535727785487,112.5101159282,112.50746382271,103.265197987482,103.108481670852,82.1717378385599,39.8194652196723,26.1110545622959,11.747772369228,6.7616217805126,5.792176967434,5.30938567918088,3.03717875752111,2.98628242844649,2.51912343716145,2.50627306818111,0.520126377735559,-0.197213805611543,-0.454975655602694,-0.465920508172833,-0.472675359537729,-0.484194786222101,-0.488852481381869,-0.524658658535558,-0.557287555019435,-0.559221879320085,-0.575248387706178],["-4.2337<br/>[-4.2453, -4.2337]","-4.2367<br/>[-4.2482, -4.2367]","-4.2333<br/>[-4.2448, -4.2333]","-4.3358<br/>[-4.3503, -4.3358]","-4.2300<br/>[-4.2413, -4.2300]","-4.2297<br/>[-4.2411, -4.2297]","-4.2291<br/>[-4.2404, -4.2291]","-4.2288<br/>[-4.2402, -4.2288]","-4.2268<br/>[-4.2382, -4.2268]","-4.2296<br/>[-4.2409, -4.2296]","-4.2295<br/>[-4.2408, -4.2295]","-4.2257<br/>[-4.2371, -4.2257]","-4.2423<br/>[-4.2541, -4.2423]","-4.2279<br/>[-4.2393, -4.2279]","-4.2227<br/>[-4.2339, -4.2227]","-4.2283<br/>[-4.2397, -4.2283]","-4.2270<br/>[-4.2385, -4.2270]","-4.2313<br/>[-4.2427, -4.2313]","-4.2247<br/>[-4.2359, -4.2247]","-4.2254<br/>[-4.2368, -4.2254]","-4.2253<br/>[-4.2367, -4.2253]","-4.2217<br/>[-4.2329, -4.2217]","-4.2217<br/>[-4.2329, -4.2217]","-4.2216<br/>[-4.2329, -4.2216]","-4.2216<br/>[-4.2329, -4.2216]","-4.2204<br/>[-4.2317, -4.2204]","-4.2209<br/>[-4.2321, -4.2209]","-4.2194<br/>[-4.2306, -4.2194]","-4.2310<br/>[-4.2424, -4.2310]","-4.2222<br/>[-4.2334, -4.2222]","-4.2380<br/>[-4.2495, -4.2380]","-4.2274<br/>[-4.2388, -4.2274]","-4.2299<br/>[-4.2413, -4.2299]","-4.2257<br/>[-4.2368, -4.2257]","-4.2259<br/>[-4.2372, -4.2259]","-4.2277<br/>[-4.2391, -4.2277]","-4.2224<br/>[-4.2336, -4.2224]","-4.2295<br/>[-4.2409, -4.2295]","-4.2230<br/>[-4.2342, -4.2230]","-4.2218<br/>[-4.2331, -4.2218]","-4.2211<br/>[-4.2324, -4.2211]","-4.2195<br/>[-4.2307, -4.2195]","-4.2210<br/>[-4.2323, -4.2210]","-4.2207<br/>[-4.2320, -4.2207]","-4.2206<br/>[-4.2319, -4.2206]","-4.2207<br/>[-4.2320, -4.2207]","-4.2195<br/>[-4.2308, -4.2195]","-4.2193<br/>[-4.2305, -4.2193]","-4.2186<br/>[-4.2298, -4.2186]"],["-3.0685<br/>[-3.0734, -3.0598]","-3.2195<br/>[-3.2317, -3.2110]","-3.2675<br/>[-3.2761, -3.2603]","-2.6164<br/>[-2.6187, -2.6145]","-3.4367<br/>[-3.4634, -3.4150]","-3.4552<br/>[-3.4774, -3.4374]","-3.5152<br/>[-3.5443, -3.4926]","-3.5351<br/>[-3.5676, -3.5084]","-3.5398<br/>[-3.5517, -3.5291]","-3.6092<br/>[-3.6526, -3.5812]","-3.6190<br/>[-3.6559, -3.5927]","-3.8079<br/>[-3.8163, -3.7976]","-2.8846<br/>[-2.8853, -2.8825]","-2.6797<br/>[-2.6797, -2.6789]","-3.4777<br/>[-3.4972, -3.4594]","-3.2442<br/>[-3.2710, -3.2186]","-3.5252<br/>[-3.5417, -3.5034]","-3.1128<br/>[-3.1155, -3.1068]","-3.5022<br/>[-3.5421, -3.4851]","-3.3641<br/>[-3.3664, -3.3581]","-3.3150<br/>[-3.3170, -3.3083]","-3.0839<br/>[-3.1117, -3.0587]","-3.1828<br/>[-3.2127, -3.1525]","-3.1885<br/>[-3.2152, -3.1602]","-3.1895<br/>[-3.2173, -3.1598]","-3.2005<br/>[-3.2032, -3.1869]","-2.4638<br/>[-2.4638, -2.4624]","-3.0315<br/>[-3.0338, -3.0153]","-2.5221<br/>[-2.5221, -2.5221]","-3.0407<br/>[-3.0588, -3.0041]","-3.1313<br/>[-3.2044, -3.0564]","-3.2900<br/>[-3.4612, -3.1693]","-3.4937<br/>[-3.5676, -3.4033]","-3.5340<br/>[-3.6110, -3.4536]","-2.1136<br/>[-2.1290, -2.1119]","-3.3522<br/>[-3.5488, -3.2227]","-3.6299<br/>[-3.8020, -3.4961]","-3.6453<br/>[-3.7893, -3.5172]","-3.9313<br/>[-4.2460, -3.7213]","-4.0843<br/>[-5.0176, -3.7712]","-4.6475<br/>[-5.9545, -4.0286]","-4.7191<br/>[-5.6050, -4.2687]","-4.7746<br/>[-6.0422, -4.1528]","-4.8000<br/>[-6.1132, -4.1647]","-4.9320<br/>[-5.7958, -4.3638]","-5.4472<br/>[-6.7800, -4.8073]","-5.5422<br/>[-6.7787, -4.9163]","-5.4716<br/>[-6.6406, -4.8803]","-5.5317<br/>[-6.6699, -4.9213]"]],"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":[["2","17","19","5","13","9","8","16","20","12","3","10","6","14","18","4","15","7","1","11"],[8697,8214,5730,11180,7410,9339,9914,9996,7905,7001,9783,8177,8609,9169,7118,12060,7549,8036,7253,10094],[1053.23157561056,504.012769179512,420.970540880808,419.875984211471,350.844832527985,320.468403414239,241.186748707687,150.773178450662,61.7038757654327,25.9057558380606,12.2149402261064,10.6875907767618,3.43661759288503,2.94139659814247,2.72013724859591,2.16296854645077,1.04535678541158,0.703438074168903,-0.452182743147458,-0.460591698878425],["-4.2379<br/>[-4.2494, -4.2379]","-4.3361<br/>[-4.3506, -4.3361]","-4.2224<br/>[-4.2337, -4.2224]","-4.2198<br/>[-4.2310, -4.2198]","-4.2424<br/>[-4.2542, -4.2424]","-4.2275<br/>[-4.2390, -4.2275]","-4.2276<br/>[-4.2391, -4.2276]","-4.2210<br/>[-4.2322, -4.2210]","-4.2282<br/>[-4.2397, -4.2282]","-4.2216<br/>[-4.2328, -4.2216]","-4.2274<br/>[-4.2389, -4.2274]","-4.2426<br/>[-4.2541, -4.2426]","-4.2303<br/>[-4.2413, -4.2303]","-4.2273<br/>[-4.2387, -4.2273]","-4.2290<br/>[-4.2404, -4.2290]","-4.2195<br/>[-4.2308, -4.2195]","-4.2213<br/>[-4.2326, -4.2213]","-4.2211<br/>[-4.2324, -4.2211]","-4.2216<br/>[-4.2328, -4.2216]","-4.2204<br/>[-4.2316, -4.2204]"],["-2.8983<br/>[-2.9011, -2.8956]","-2.6811<br/>[-2.6872, -2.6764]","-3.2277<br/>[-3.2678, -3.1957]","-3.5691<br/>[-3.5708, -3.5664]","-2.9056<br/>[-2.9059, -2.9043]","-3.1172<br/>[-3.1225, -3.1123]","-3.4309<br/>[-3.4812, -3.3973]","-2.5632<br/>[-2.5815, -2.5632]","-3.3308<br/>[-3.3638, -3.2713]","-2.5116<br/>[-2.5116, -2.4907]","-2.1697<br/>[-2.1947, -2.1697]","-3.0085<br/>[-3.1026, -2.9182]","-3.3157<br/>[-3.4585, -3.1751]","-3.4304<br/>[-3.6407, -3.2768]","-3.1167<br/>[-3.4762, -2.9831]","-3.7273<br/>[-4.0624, -3.5032]","-3.6984<br/>[-3.8689, -3.5239]","-3.7280<br/>[-4.0594, -3.4969]","-4.6406<br/>[-5.4281, -4.1953]","-4.6168<br/>[-5.5037, -4.0804]"]],"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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