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<title>Enrichment results of Alzheimer’s disease</title>

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<h1 class="title toc-ignore">Enrichment results of Alzheimer’s 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> 2018-06-27</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/24162737">“Meta-Analysis of 74,046 Individuals Identifies 11 New Susceptibility Loci for Alzheimer’s Disease” (<em>Nature Genetics</em>, 2013)</a>. The summary data file is available at <a href="http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php" class="uri">http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php</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>
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IFN<br/>(reactome, BioSystems)","Regulation of innate immune responses to cytosolic DNA<br/>(reactome, PC)","Regulation of innate immune responses to cytosolic DNA<br/>(reactome, BioSystems)","EGF receptor signaling pathway<br/>(panther, PANTHER)","Ubiquitin mediated proteolysis<br/>(kegg, BioSystems)","EGF receptor signaling pathway<br/>(panther, PC)","Insulin signaling pathway<br/>(kegg, BioSystems)","EGFR1 Signaling Pathway<br/>(wiki, BioSystems)","Endocytosis<br/>(kegg, BioSystems)","Synthesis of 5-eicosatetraenoic acids<br/>(reactome, PC)","Biotin metabolism<br/>(kegg, PC)","Biotin metabolism<br/>(kegg, BioSystems)","tetrapyrrole biosynthesis<br/>(humancyc, PC)","ATM mediated phosphorylation of repair proteins<br/>(reactome, PC)","Abacavir metabolism<br/>(reactome, PC)","TRAMP complex<br/>(kegg, BioSystems)","Pyruvate metabolism<br/>(panther, PC)","GRB7 events in ERBB2 signaling<br/>(reactome, PC)","Neuroregulin receptor degredation protein-1 Controls ErbB3 receptor recycling<br/>(biocarta, BioCarta)"],[3,4,3,4,8,6,49,10,9,11,11,10,10,11,14,13,14,13,14,14,17,16,16,16,22,17,30,17,16,22,30,28,28,30,36,33,33,31,33,37,19,7,19,49,47,41,40,51,25,69,31,30,42,30,17,93,40,15,39,40,30,59,30,82,83,72,88,89,50,58,181,174,52,71,76,101,6,84,15,148,13,14,15,16,99,128,108,133,169,252,6,2,3,4,5,5,4,7,5,5],[294,342,370,416,457,567,5238,615,805,894,950,1019,1209,1332,1424,1476,1543,1653,1713,1790,1774,1867,1917,1893,1941,1980,2561,2073,2063,2240,2581,2958,3022,3185,3119,3277,3381,3313,3372,3703,1802,765,2643,4025,4004,4903,4825,5608,3322,3996,3483,6144,5206,3952,1331,5227,4930,1730,5090,5090,2742,9002,3035,11967,11967,10591,10159,10159,4594,5155,16843,12608,7329,7521,9986,10395,567,11309,1117,11259,1152,1163,1328,1339,12510,12729,13332,13108,18112,26056,543,283,341,341,357,491,481,594,868,1102],[91.3586182940517,91.1698645263379,90.9533149078856,90.8539252299794,90.4314929865099,86.7115247045063,83.7356918219519,80.3313192170224,80.0322028589396,79.9651817775757,79.900914040804,79.8322357117316,79.7297557279262,79.6279922564124,79.5734733565544,79.5410750964556,79.4735748054127,79.4510624542773,79.4008481772513,79.3630407469422,79.3579727482107,79.3292014115323,79.3139589641547,79.3118991809961,79.3111015904443,79.2910416969663,79.2837189831319,79.2498935538083,79.2371185127566,79.1985068917819,79.0778592873268,78.9538480217768,78.9352927773488,78.9121014201369,78.8992418017117,78.8593990400095,78.8587692565755,78.8397102348434,78.8193686897841,78.7397321540782,61.7184381618253,60.8392861565332,57.1529511956187,54.3520278657297,54.3253529488028,52.9697363162565,52.8622036298312,51.8841877323194,47.4529534810132,46.0564780944655,45.0391960747378,44.360443993375,44.3522062573813,43.8076973059303,43.7945177895497,43.6743501314515,43.0379024262025,41.7679104643282,40.6147263522201,40.6147263522201,38.2767167977028,37.7777034143681,37.5044669339185,36.047526498282,36.047526498282,35.6367528575296,34.6763833239986,34.6763833239986,34.6225689078732,33.8823271409916,33.65243476009,33.5433661893205,33.3157172878431,32.805152161779,31.8849788080017,30.5830870466936,30.4440448142418,30.3383229299628,30.2082146607131,30.0952765150179,29.9505671046568,29.9402383419512,29.8119032496313,29.7914432713531,29.782774583122,29.4533249913705,29.3471122261266,29.1657134484775,28.248121893619,28.0545256320559,0.700298683442577,-0.208820249777997,-0.223596393927042,-0.224929236468593,-0.227627550104773,-0.252584288649357,-0.253128784403795,-0.270687216888412,-0.286940706419334,-0.314181528159898],["-4.5552<br/>[-4.5564, -4.5480]","-4.5551<br/>[-4.5563, -4.5480]","-4.5551<br/>[-4.5563, -4.5480]","-4.5551<br/>[-4.5563, -4.5479]","-4.5551<br/>[-4.5563, -4.5479]","-4.5551<br/>[-4.5563, -4.5479]","-4.5842<br/>[-4.5853, -4.5773]","-4.5550<br/>[-4.5562, -4.5479]","-4.5550<br/>[-4.5562, -4.5478]","-4.5549<br/>[-4.5561, -4.5478]","-4.5549<br/>[-4.5561, -4.5477]","-4.5549<br/>[-4.5561, -4.5477]","-4.5548<br/>[-4.5560, -4.5476]","-4.5548<br/>[-4.5560, -4.5476]","-4.5547<br/>[-4.5559, -4.5476]","-4.5547<br/>[-4.5559, -4.5475]","-4.5547<br/>[-4.5559, -4.5475]","-4.5546<br/>[-4.5558, -4.5475]","-4.5546<br/>[-4.5558, -4.5474]","-4.5546<br/>[-4.5558, -4.5474]","-4.5546<br/>[-4.5558, -4.5474]","-4.5546<br/>[-4.5558, -4.5474]","-4.5545<br/>[-4.5557, -4.5474]","-4.5546<br/>[-4.5558, -4.5474]","-4.5545<br/>[-4.5557, -4.5474]","-4.5545<br/>[-4.5557, -4.5473]","-4.5546<br/>[-4.5558, -4.5475]","-4.5545<br/>[-4.5557, -4.5473]","-4.5545<br/>[-4.5557, -4.5473]","-4.5544<br/>[-4.5556, -4.5473]","-4.5543<br/>[-4.5555, -4.5471]","-4.5542<br/>[-4.5554, -4.5470]","-4.5541<br/>[-4.5553, -4.5470]","-4.5541<br/>[-4.5553, -4.5469]","-4.5541<br/>[-4.5553, -4.5469]","-4.5540<br/>[-4.5552, -4.5469]","-4.5540<br/>[-4.5552, -4.5469]","-4.5540<br/>[-4.5552, -4.5469]","-4.5540<br/>[-4.5552, -4.5468]","-4.5539<br/>[-4.5551, -4.5467]","-4.8619<br/>[-4.8642, -4.8479]","-4.9228<br/>[-4.9256, -4.9066]","-4.8612<br/>[-4.8635, -4.8471]","-4.8611<br/>[-4.8635, -4.8468]","-4.8611<br/>[-4.8635, -4.8468]","-4.8604<br/>[-4.8627, -4.8464]","-4.8604<br/>[-4.8627, -4.8464]","-4.8605<br/>[-4.8629, -4.8462]","-4.9219<br/>[-4.9247, -4.9057]","-4.9217<br/>[-4.9244, -4.9054]","-4.9209<br/>[-4.9236, -4.9045]","-4.9208<br/>[-4.9236, -4.9046]","-4.9538<br/>[-4.9568, -4.9365]","-4.9217<br/>[-4.9244, -4.9054]","-4.8754<br/>[-4.8777, -4.8618]","-4.9284<br/>[-4.9310, -4.9132]","-4.9539<br/>[-4.9569, -4.9366]","-4.8753<br/>[-4.8775, -4.8617]","-4.8927<br/>[-4.8949, -4.8799]","-4.8927<br/>[-4.8949, -4.8799]","-4.8749<br/>[-4.8772, -4.8613]","-4.9198<br/>[-4.9225, -4.9036]","-4.8748<br/>[-4.8771, -4.8612]","-4.9196<br/>[-4.9223, -4.9036]","-4.9196<br/>[-4.9223, -4.9036]","-4.9183<br/>[-4.9210, -4.9019]","-4.8909<br/>[-4.8930, -4.8781]","-4.8909<br/>[-4.8930, -4.8781]","-4.8743<br/>[-4.8766, -4.8608]","-4.8741<br/>[-4.8764, -4.8606]","-4.7469<br/>[-4.7486, -4.7367]","-4.9179<br/>[-4.9207, -4.9017]","-4.8076<br/>[-4.8098, -4.7947]","-4.8065<br/>[-4.8087, -4.7935]","-4.8232<br/>[-4.8253, -4.8108]","-4.8054<br/>[-4.8076, -4.7924]","-4.5551<br/>[-4.5563, -4.5479]","-4.8062<br/>[-4.8083, -4.7933]","-4.5552<br/>[-4.5564, -4.5480]","-4.8051<br/>[-4.8073, -4.7922]","-4.5549<br/>[-4.5561, -4.5477]","-4.5549<br/>[-4.5561, -4.5477]","-4.5548<br/>[-4.5560, -4.5477]","-4.5548<br/>[-4.5560, -4.5477]","-4.8058<br/>[-4.8079, -4.7929]","-4.8047<br/>[-4.8069, -4.7918]","-4.8054<br/>[-4.8076, -4.7926]","-4.8045<br/>[-4.8066, -4.7915]","-4.8061<br/>[-4.8082, -4.7937]","-4.8532<br/>[-4.8557, -4.8389]","-4.5565<br/>[-4.5577, -4.5496]","-4.5552<br/>[-4.5564, -4.5480]","-4.5551<br/>[-4.5563, -4.5480]","-4.5551<br/>[-4.5563, -4.5480]","-4.5551<br/>[-4.5563, -4.5480]","-4.5551<br/>[-4.5563, -4.5479]","-4.5551<br/>[-4.5563, -4.5479]","-4.5550<br/>[-4.5562, -4.5479]","-4.5549<br/>[-4.5561, -4.5478]","-4.5549<br/>[-4.5561, -4.5477]"],["-1.9762<br/>[-1.9888, -1.9620]","-2.0426<br/>[-2.0547, -2.0292]","-2.0674<br/>[-2.0781, -2.0512]","-2.1279<br/>[-2.1367, -2.1155]","-2.1622<br/>[-2.1682, -2.1517]","-2.2196<br/>[-2.2234, -2.2107]","-2.7489<br/>[-2.7489, -2.7483]","-2.4506<br/>[-2.4875, -2.4391]","-2.5918<br/>[-2.6043, -2.5747]","-2.6339<br/>[-2.6496, -2.6118]","-2.6626<br/>[-2.6765, -2.6441]","-2.6941<br/>[-2.7066, -2.6768]","-2.7693<br/>[-2.7809, -2.7528]","-2.8122<br/>[-2.8230, -2.7965]","-2.8406<br/>[-2.8520, -2.8240]","-2.8563<br/>[-2.8677, -2.8403]","-2.8771<br/>[-2.8869, -2.8628]","-2.9067<br/>[-2.9167, -2.8917]","-2.9226<br/>[-2.9324, -2.9086]","-2.9414<br/>[-2.9515, -2.9269]","-2.9377<br/>[-2.9475, -2.9236]","-2.9605<br/>[-2.9699, -2.9472]","-2.9720<br/>[-2.9811, -2.9583]","-2.9666<br/>[-2.9757, -2.9531]","-2.9764<br/>[-2.9868, -2.9621]","-2.9859<br/>[-2.9954, -2.9726]","-3.0149<br/>[-3.0915, -2.9538]","-3.0061<br/>[-3.0153, -2.9932]","-3.0037<br/>[-3.0130, -2.9898]","-3.0319<br/>[-3.0484, -3.0089]","-3.1008<br/>[-3.1102, -3.0866]","-3.1594<br/>[-3.1696, -3.1447]","-3.1687<br/>[-3.1789, -3.1541]","-3.1869<br/>[-3.2013, -3.1672]","-3.1811<br/>[-3.1926, -3.1648]","-3.2039<br/>[-3.2140, -3.1894]","-3.2068<br/>[-3.2262, -3.1789]","-3.2076<br/>[-3.2182, -3.1914]","-3.2177<br/>[-3.2265, -3.2050]","-3.2586<br/>[-3.2670, -3.2462]","-1.9085<br/>[-1.9155, -1.8999]","-1.4863<br/>[-1.4877, -1.4839]","-2.1008<br/>[-2.1056, -2.0974]","-2.2919<br/>[-2.2987, -2.2776]","-2.2805<br/>[-2.2961, -2.2742]","-2.3771<br/>[-2.3842, -2.3545]","-2.3703<br/>[-2.3775, -2.3550]","-2.4309<br/>[-2.4421, -2.4184]","-2.1285<br/>[-2.1344, -2.1261]","-2.2093<br/>[-2.2126, -2.2075]","-2.1712<br/>[-2.1741, -2.1694]","-2.4281<br/>[-2.4282, -2.4271]","-2.3071<br/>[-2.3149, -2.2992]","-2.2139<br/>[-2.2170, -2.2126]","-1.7872<br/>[-1.7978, -1.7763]","-2.3177<br/>[-2.3208, -2.3090]","-2.2840<br/>[-2.3072, -2.2765]","-1.9054<br/>[-1.9128, -1.8942]","-2.3451<br/>[-2.3551, -2.3324]","-2.3451<br/>[-2.3551, -2.3324]","-2.1057<br/>[-2.1128, -2.1009]","-2.5710<br/>[-2.5714, -2.5702]","-2.1514<br/>[-2.1601, -2.1403]","-2.6774<br/>[-2.6821, -2.6720]","-2.6774<br/>[-2.6821, -2.6720]","-2.6810<br/>[-2.6835, -2.6581]","-2.6567<br/>[-2.6587, -2.6484]","-2.6567<br/>[-2.6587, -2.6484]","-2.3435<br/>[-2.3523, -2.3247]","-2.3805<br/>[-2.3985, -2.3640]","-2.9394<br/>[-2.9412, -2.9321]","-2.7407<br/>[-2.7433, -2.7388]","-2.6462<br/>[-2.6614, -2.6150]","-2.6786<br/>[-2.6894, -2.6682]","-2.7766<br/>[-2.7870, -2.7683]","-2.8242<br/>[-2.8304, -2.8170]","-2.4067<br/>[-2.4505, -2.3494]","-2.8454<br/>[-2.8561, -2.8362]","-2.6050<br/>[-2.6841, -2.5285]","-2.8554<br/>[-2.8631, -2.8471]","-2.6673<br/>[-2.7488, -2.5765]","-2.6718<br/>[-2.7533, -2.5828]","-2.6892<br/>[-2.7670, -2.5855]","-2.6916<br/>[-2.7676, -2.5884]","-2.8874<br/>[-2.8979, -2.8762]","-2.9028<br/>[-2.9109, -2.8933]","-2.9159<br/>[-2.9249, -2.9053]","-2.9240<br/>[-2.9296, -2.9177]","-3.0225<br/>[-3.0385, -3.0058]","-3.1547<br/>[-3.1645, -3.1460]","-2.6386<br/>[-3.6806, -2.4293]","-4.3421<br/>[-6.3416, -3.6572]","-4.4501<br/>[-6.3810, -3.7727]","-4.5876<br/>[-6.5065, -3.9136]","-4.5105<br/>[-6.4180, -3.8338]","-4.5615<br/>[-6.3539, -3.8948]","-4.7704<br/>[-6.5744, -4.1021]","-4.8129<br/>[-6.5436, -4.1512]","-4.2408<br/>[-5.7769, -3.6127]","-4.4360<br/>[-5.9222, -3.7997]"]],"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 &pi;<br/>(mean, 95% CI)<\/th>\n      <th>Log10 inside &pi;<br/>(mean, 95% CI)<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 3, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-highly-expressed-genes" class="section level3">
<h3>Tissue highly expressed genes</h3>
<div id="htmlwidget-0aaad034f4771159c3b9" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-0aaad034f4771159c3b9">{"x":{"filter":"none","data":[["Liver","Brain - Cortex","Adrenal Gland","Brain - Frontal Cortex (BA9)","Brain - Hippocampus","Brain - Cerebellum","Brain - Anterior cingulate cortex (BA24)","Brain - Hypothalamus","Brain - Caudate (basal ganglia)","Brain - Nucleus accumbens (basal ganglia)","Brain - Putamen (basal ganglia)","Muscle - Skeletal","Testis","Brain - Cerebellar Hemisphere","Artery - Tibial","Artery - Aorta","Thyroid","Heart - Atrial Appendage","Heart - Left Ventricle","Whole Blood","Spleen","Cells - EBV-transformed lymphocytes","Colon - Transverse","Esophagus - Gastroesophageal Junction","Colon - Sigmoid","Esophagus - Muscularis","Small Intestine - Terminal Ileum","Lung","Pancreas","Cells - Transformed fibroblasts","Stomach","Esophagus - Mucosa","Prostate","Breast - Mammary Tissue","Vagina","Adipose - Subcutaneous","Skin - Sun Exposed (Lower leg)","Nerve - Tibial","Uterus","Skin - Not Sun Exposed (Suprapubic)","Adipose - Visceral (Omentum)","Pituitary","Ovary","Artery - Coronary"],[7064,6736,6456,7036,6532,6583,6738,6611,7335,6929,7419,6531,6786,6413,6797,7082,6967,6672,6469,6567,4629,5702,6021,6576,6687,6779,5320,5632,5809,6925,6019,6301,6422,6375,6546,6395,6527,6481,6515,6632,6630,6698,6760,6945],[37.7927084607987,32.7105928280704,31.9992402255046,31.9005237743841,31.8319061319515,31.5532272862588,31.3927554841698,31.3648798087792,30.9141242695713,30.803118724609,30.7429472922083,3.81009882482412,2.89515761107549,1.99992312669165,1.91892986379533,1.91049993863164,1.8768634871007,0.374460941000413,0.348562528404843,-0.405453289481714,-0.413893009982755,-0.452855990222728,-0.4536085001802,-0.473794388922644,-0.476337156947924,-0.479130889680384,-0.481370077031587,-0.495847497805131,-0.5015084003497,-0.501707948940717,-0.503499478453694,-0.50575232521017,-0.512598628533733,-0.512968704078661,-0.513498046282594,-0.514333759616917,-0.515978785249235,-0.516594113235675,-0.516936668245663,-0.517853591092259,-0.518530423588226,-0.521032239473646,-0.523065430188074,-0.525282928327843],["-4.9400<br/>[-4.9425, -4.9246]","-4.9194<br/>[-4.9221, -4.9034]","-4.9194<br/>[-4.9222, -4.9034]","-4.9191<br/>[-4.9218, -4.9031]","-4.9194<br/>[-4.9221, -4.9034]","-4.9193<br/>[-4.9221, -4.9033]","-4.9192<br/>[-4.9220, -4.9032]","-4.9194<br/>[-4.9221, -4.9034]","-4.9192<br/>[-4.9219, -4.9032]","-4.9193<br/>[-4.9220, -4.9033]","-4.9191<br/>[-4.9218, -4.9031]","-4.5827<br/>[-4.5840, -4.5749]","-4.5828<br/>[-4.5840, -4.5754]","-4.5813<br/>[-4.5826, -4.5737]","-4.5811<br/>[-4.5824, -4.5735]","-4.5810<br/>[-4.5823, -4.5734]","-4.5811<br/>[-4.5823, -4.5734]","-4.5544<br/>[-4.5556, -4.5470]","-4.5544<br/>[-4.5556, -4.5470]","-4.5536<br/>[-4.5548, -4.5466]","-4.5539<br/>[-4.5551, -4.5468]","-4.5535<br/>[-4.5547, -4.5464]","-4.5534<br/>[-4.5546, -4.5463]","-4.5532<br/>[-4.5544, -4.5461]","-4.5531<br/>[-4.5543, -4.5460]","-4.5531<br/>[-4.5543, -4.5460]","-4.5533<br/>[-4.5545, -4.5462]","-4.5532<br/>[-4.5544, -4.5461]","-4.5531<br/>[-4.5543, -4.5460]","-4.5528<br/>[-4.5540, -4.5457]","-4.5531<br/>[-4.5543, -4.5459]","-4.5530<br/>[-4.5542, -4.5458]","-4.5529<br/>[-4.5541, -4.5458]","-4.5529<br/>[-4.5541, -4.5458]","-4.5529<br/>[-4.5541, -4.5457]","-4.5529<br/>[-4.5541, -4.5458]","-4.5529<br/>[-4.5541, -4.5457]","-4.5529<br/>[-4.5541, -4.5457]","-4.5529<br/>[-4.5541, -4.5457]","-4.5528<br/>[-4.5540, -4.5457]","-4.5528<br/>[-4.5540, -4.5457]","-4.5528<br/>[-4.5540, -4.5457]","-4.5528<br/>[-4.5540, -4.5456]","-4.5527<br/>[-4.5539, -4.5456]"],["-2.4460<br/>[-2.4525, -2.4376]","-2.4574<br/>[-2.4686, -2.4563]","-2.4441<br/>[-2.4602, -2.4394]","-2.4787<br/>[-2.4937, -2.4773]","-2.4500<br/>[-2.4645, -2.4435]","-2.4552<br/>[-2.4651, -2.4442]","-2.4661<br/>[-2.4755, -2.4589]","-2.4627<br/>[-2.4736, -2.4480]","-2.5008<br/>[-2.5132, -2.4918]","-2.4818<br/>[-2.4941, -2.4656]","-2.5043<br/>[-2.5182, -2.4968]","-3.2074<br/>[-3.3143, -3.1263]","-3.2677<br/>[-3.4048, -3.1674]","-3.4222<br/>[-3.4959, -3.3329]","-3.4594<br/>[-3.5238, -3.3771]","-3.4638<br/>[-3.5404, -3.3666]","-3.4804<br/>[-3.5380, -3.4138]","-3.6979<br/>[-3.9779, -3.5317]","-3.7152<br/>[-4.0010, -3.5784]","-4.3413<br/>[-4.9826, -3.8924]","-4.4153<br/>[-5.1719, -3.8706]","-4.5752<br/>[-5.2650, -4.1685]","-4.5392<br/>[-5.2610, -4.1074]","-4.6308<br/>[-5.3115, -4.2009]","-4.6377<br/>[-5.3171, -4.2019]","-4.6497<br/>[-5.3237, -4.2386]","-4.8599<br/>[-5.7942, -4.3299]","-5.0029<br/>[-5.8984, -4.4839]","-5.0457<br/>[-5.9267, -4.5174]","-4.7605<br/>[-5.6541, -4.2225]","-4.9955<br/>[-5.8898, -4.4560]","-4.9404<br/>[-5.8379, -4.3931]","-5.0200<br/>[-5.9019, -4.4969]","-5.0464<br/>[-5.9210, -4.5252]","-4.9964<br/>[-5.8749, -4.4718]","-5.0677<br/>[-5.9359, -4.5454]","-5.0487<br/>[-5.9207, -4.5203]","-5.0807<br/>[-5.9443, -4.5542]","-5.0736<br/>[-5.9393, -4.5454]","-5.0460<br/>[-5.9181, -4.5127]","-5.0609<br/>[-5.9285, -4.5276]","-5.0873<br/>[-5.9472, -4.5506]","-5.1070<br/>[-5.9603, -4.5812]","-5.0803<br/>[-5.9394, -4.5687]"]],"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 &pi;<br/>(mean, 95% CI)<\/th>\n      <th>Log10 inside &pi;<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":[["Adrenal_Gland","Liver","Vagina","Esophagus_Mucosa","Pancreas","Breast_Mammary_Tissue","Muscle_Skeletal","Cells_EBV-transformed_lymphocytes","Spleen","Heart_Atrial_Appendage","Brain_Spinal_cord_(cervical_c-1)","Heart_Left_Ventricle","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Prostate","Whole_Blood","Kidney_Cortex","Stomach","Minor_Salivary_Gland","Colon_Transverse","Adipose_Visceral_(Omentum)","Testis","Lung","Thyroid","Small_Intestine_Terminal_Ileum","Pituitary","Colon_Sigmoid","Cells_Transformed_fibroblasts","Brain_Cerebellum","Artery_Coronary","Brain_Hippocampus","Brain_Amygdala","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Cortex","Ovary","Uterus","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Hypothalamus","Nerve_Tibial","Artery_Aorta","Artery_Tibial","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Substantia_nigra","Brain_Frontal_Cortex_(BA9)","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis","Brain_Cerebellar_Hemisphere","Adipose_Subcutaneous"],[13238,9009,7397,7499,8331,10616,9537,8497,7956,11935,13582,11889,7357,7449,9956,7978,9769,10134,9223,8372,10715,8598,9113,12944,9584,10458,11710,11473,11828,13319,11965,12151,12323,12963,12476,13417,12643,12731,13161,13428,15254,13482,14052,13613,14628,14960,15089,14440,10896],[45.6085155230252,31.1512071172765,5.11765163671145,5.11194441150148,5.0186021712066,4.75882999382297,1.65669033490724,0.42644470248261,0.332824759032967,0.115295980179201,0.103928460533598,0.044195329051038,-0.122269701737504,-0.124445287290412,-0.310575836799704,-0.498973686969832,-0.528109415720381,-0.540458920439887,-0.549257174967806,-0.559279314588254,-0.560539183401918,-0.56125372275826,-0.562818925296933,-0.575776875418586,-0.581770501228713,-0.597571766471057,-0.607155258882123,-0.608569971667429,-0.61456610570706,-0.615602972664737,-0.616965321646786,-0.620030963626182,-0.62293883921788,-0.624641589017718,-0.625226249925018,-0.626661186984941,-0.627132579930623,-0.62769782932844,-0.628476949325879,-0.629069438842651,-0.630991934265566,-0.635889268935661,-0.63772292690542,-0.639017015755406,-0.64574090597378,-0.649495059043024,-0.649712191619083,-0.651509365678129,-0.952695975773879],["-4.8572<br/>[-4.8596, -4.8432]","-4.8185<br/>[-4.8206, -4.8065]","-4.5614<br/>[-4.5625, -4.5547]","-4.5613<br/>[-4.5624, -4.5547]","-4.5611<br/>[-4.5622, -4.5544]","-4.5601<br/>[-4.5612, -4.5534]","-4.5674<br/>[-4.5686, -4.5599]","-4.5662<br/>[-4.5675, -4.5589]","-4.5662<br/>[-4.5674, -4.5588]","-4.5526<br/>[-4.5538, -4.5453]","-4.5639<br/>[-4.5652, -4.5566]","-4.5523<br/>[-4.5535, -4.5450]","-4.5525<br/>[-4.5537, -4.5454]","-4.5525<br/>[-4.5537, -4.5453]","-4.5528<br/>[-4.5540, -4.5459]","-4.5527<br/>[-4.5539, -4.5456]","-4.5522<br/>[-4.5533, -4.5451]","-4.5517<br/>[-4.5529, -4.5446]","-4.5520<br/>[-4.5531, -4.5448]","-4.5521<br/>[-4.5533, -4.5450]","-4.5515<br/>[-4.5527, -4.5445]","-4.5521<br/>[-4.5533, -4.5449]","-4.5519<br/>[-4.5531, -4.5448]","-4.5508<br/>[-4.5520, -4.5438]","-4.5517<br/>[-4.5529, -4.5445]","-4.5513<br/>[-4.5525, -4.5442]","-4.5509<br/>[-4.5521, -4.5438]","-4.5510<br/>[-4.5522, -4.5438]","-4.5508<br/>[-4.5520, -4.5437]","-4.5504<br/>[-4.5516, -4.5432]","-4.5508<br/>[-4.5520, -4.5436]","-4.5507<br/>[-4.5519, -4.5435]","-4.5506<br/>[-4.5518, -4.5435]","-4.5504<br/>[-4.5516, -4.5433]","-4.5506<br/>[-4.5518, -4.5434]","-4.5503<br/>[-4.5515, -4.5431]","-4.5505<br/>[-4.5517, -4.5433]","-4.5505<br/>[-4.5517, -4.5433]","-4.5503<br/>[-4.5515, -4.5432]","-4.5503<br/>[-4.5515, -4.5431]","-4.5497<br/>[-4.5509, -4.5426]","-4.5502<br/>[-4.5514, -4.5430]","-4.5500<br/>[-4.5512, -4.5429]","-4.5501<br/>[-4.5513, -4.5430]","-4.5498<br/>[-4.5510, -4.5426]","-4.5497<br/>[-4.5509, -4.5425]","-4.5496<br/>[-4.5508, -4.5425]","-4.5498<br/>[-4.5510, -4.5426]","-4.5653<br/>[-4.5665, -4.5579]"],["-2.8125<br/>[-2.8177, -2.8071]","-2.6982<br/>[-2.7264, -2.6794]","-3.5159<br/>[-3.5594, -3.4535]","-3.5105<br/>[-3.5608, -3.4405]","-3.5540<br/>[-3.5964, -3.4947]","-3.6883<br/>[-3.7182, -3.6418]","-3.5355<br/>[-3.6609, -3.4040]","-3.7862<br/>[-3.9188, -3.6102]","-3.8620<br/>[-3.8988, -3.7915]","-3.9703<br/>[-4.2658, -3.7902]","-4.0869<br/>[-4.1348, -4.0059]","-4.0252<br/>[-4.3001, -3.9039]","-3.9603<br/>[-4.5335, -3.7541]","-3.9630<br/>[-4.5382, -3.7522]","-4.1485<br/>[-4.8889, -3.8152]","-4.7136<br/>[-5.2877, -4.2962]","-4.7084<br/>[-5.3149, -4.2830]","-4.7733<br/>[-5.4814, -4.2680]","-4.9171<br/>[-5.7656, -4.3823]","-5.2880<br/>[-6.1474, -4.7657]","-4.8633<br/>[-5.6675, -4.3526]","-5.2380<br/>[-6.1146, -4.7049]","-5.1443<br/>[-5.9078, -4.6472]","-4.8453<br/>[-5.4521, -4.3515]","-5.3962<br/>[-6.2173, -4.8691]","-5.4928<br/>[-6.3160, -4.9650]","-5.3014<br/>[-6.0985, -4.7589]","-5.4105<br/>[-6.2054, -4.8653]","-5.4569<br/>[-6.2309, -4.9463]","-5.1558<br/>[-5.8642, -4.6675]","-5.4716<br/>[-6.2586, -4.9500]","-5.4951<br/>[-6.2770, -4.9676]","-5.5212<br/>[-6.2968, -4.9887]","-5.3607<br/>[-6.1220, -4.8308]","-5.5331<br/>[-6.3098, -4.9944]","-5.3072<br/>[-6.0279, -4.8063]","-5.5297<br/>[-6.2993, -5.0056]","-5.5130<br/>[-6.2819, -4.9880]","-5.3922<br/>[-6.1602, -4.8668]","-5.3574<br/>[-6.0646, -4.8800]","-5.1062<br/>[-5.8105, -4.6233]","-5.4950<br/>[-6.2454, -4.9831]","-5.3805<br/>[-6.1229, -4.8680]","-5.5437<br/>[-6.2944, -5.0237]","-5.4234<br/>[-6.1524, -4.8970]","-5.4273<br/>[-6.1575, -4.9082]","-5.4015<br/>[-6.1319, -4.9068]","-5.6565<br/>[-6.3913, -5.1554]","-3.9443<br/>[-4.0295, -3.8270]"]],"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 &pi;<br/>(mean, 95% CI)<\/th>\n      <th>Log10 inside &pi;<br/>(mean, 95% CI)<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="cluster-distinctively-expressed-genes" class="section level3">
<h3>Cluster distinctively expressed genes</h3>
<div id="htmlwidget-798b325e8770e69abc2e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-798b325e8770e69abc2e">{"x":{"filter":"none","data":[["20","15","7","9","17","6","1","19","13","18","12","14","10","8","11","2","5","3","16","4"],[9013,8561,9192,10371,9466,9826,8425,6525,8572,7978,7827,10199,9288,10988,11253,10164,12371,11002,11079,13143],[35.7337808235818,4.19334280855615,3.28801385738683,1.57800945218343,0.561757953203187,-0.241667141242856,-0.413624885369376,-0.462411491435854,-0.502889206447826,-0.508161340713624,-0.512265433057215,-0.513241474695057,-0.538986693678825,-0.546511468036385,-0.553264413327841,-0.554216555977288,-0.566775231698589,-0.570073473445587,-0.572578497854439,-0.587087789388652],["-4.8769<br/>[-4.8792, -4.8636]","-4.5524<br/>[-4.5536, -4.5453]","-4.5817<br/>[-4.5830, -4.5739]","-4.5798<br/>[-4.5811, -4.5722]","-4.5664<br/>[-4.5676, -4.5592]","-4.5529<br/>[-4.5541, -4.5461]","-4.5528<br/>[-4.5539, -4.5457]","-4.5530<br/>[-4.5542, -4.5459]","-4.5522<br/>[-4.5534, -4.5451]","-4.5523<br/>[-4.5535, -4.5452]","-4.5524<br/>[-4.5536, -4.5452]","-4.5519<br/>[-4.5531, -4.5448]","-4.5518<br/>[-4.5530, -4.5447]","-4.5513<br/>[-4.5525, -4.5442]","-4.5512<br/>[-4.5524, -4.5441]","-4.5515<br/>[-4.5527, -4.5443]","-4.5507<br/>[-4.5519, -4.5436]","-4.5511<br/>[-4.5523, -4.5440]","-4.5511<br/>[-4.5523, -4.5439]","-4.5504<br/>[-4.5516, -4.5433]"],["-2.6000<br/>[-2.6064, -2.5835]","-3.3895<br/>[-3.3951, -3.3895]","-3.3817<br/>[-3.4757, -3.3052]","-3.6512<br/>[-3.7079, -3.5804]","-3.7528<br/>[-3.9482, -3.5826]","-4.0708<br/>[-4.8956, -3.7213]","-4.3951<br/>[-5.1346, -3.8967]","-4.7960<br/>[-5.6080, -4.3067]","-4.9006<br/>[-5.6544, -4.4265]","-5.0542<br/>[-5.9026, -4.5392]","-5.1744<br/>[-6.0407, -4.6445]","-4.8703<br/>[-5.4002, -4.4686]","-5.2487<br/>[-6.1064, -4.6940]","-5.0125<br/>[-5.8202, -4.4877]","-5.0863<br/>[-5.7986, -4.6156]","-5.3110<br/>[-6.1491, -4.7610]","-5.0831<br/>[-5.8170, -4.5714]","-5.4347<br/>[-6.2442, -4.8925]","-5.4804<br/>[-6.2898, -4.9638]","-5.2482<br/>[-5.9761, -4.7370]"]],"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 &pi;<br/>(mean, 95% CI)<\/th>\n      <th>Log10 inside &pi;<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&amp;id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DT_0.4         plyr_1.8.4     dplyr_0.7.5    R.matlab_3.6.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      compiler_3.5.0    pillar_1.2.3     
 [4] later_0.7.3       git2r_0.21.0      workflowr_1.0.1  
 [7] bindr_0.1.1       R.methodsS3_1.7.1 R.utils_2.6.0    
[10] tools_3.5.0       digest_0.6.15     jsonlite_1.5     
[13] evaluate_0.10.1   tibble_1.4.2      pkgconfig_2.0.1  
[16] rlang_0.2.1       shiny_1.1.0       crosstalk_1.0.0  
[19] yaml_2.1.19       bindrcpp_0.2.2    stringr_1.3.1    
[22] knitr_1.20        htmlwidgets_1.2   rprojroot_1.3-2  
[25] tidyselect_0.2.4  glue_1.2.0        R6_2.2.2         
[28] rmarkdown_1.10    purrr_0.2.5       magrittr_1.5     
[31] whisker_0.3-2     backports_1.1.2   promises_1.0.1   
[34] htmltools_0.3.6   assertthat_0.2.0  mime_0.5         
[37] xtable_1.8-2      httpuv_1.4.4.1    stringi_1.2.3    
[40] R.oo_1.22.0      </code></pre>
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