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<h1 class="title toc-ignore">Enrichment results of neuroticism</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/27089181">“Genetic Variants Associated with Subjective Well-Being, Depressive Symptoms, and Neuroticism Identified Through Genome-Wide Analyses” (<em>Nature Genetics</em>, 2016)</a>. The summary data file is available at <a href="https://www.thessgac.org/data" class="uri">https://www.thessgac.org/data</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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BioSystems)","Beta defensins<br/>(reactome, PC)","Beta defensins<br/>(reactome, BioSystems)","Axon guidance<br/>(kegg, BioSystems)","Defensins<br/>(reactome, PC)","Defensins<br/>(reactome, BioSystems)","Colorectal cancer<br/>(kegg, BioSystems)","Nuclear pore complex<br/>(kegg, BioSystems)","Cross-presentation of soluble exogenous antigens (endosomes)<br/>(reactome, PC)","Cross-presentation of soluble exogenous antigens (endosomes)<br/>(reactome, BioSystems)","Rev-mediated nuclear export of HIV RNA<br/>(reactome, PC)","Proteasome<br/>(kegg, BioSystems)","Regulation of Apoptosis<br/>(reactome, BioSystems)","Interactions of Rev with host cellular proteins<br/>(reactome, PC)","Rev-mediated nuclear export of HIV RNA<br/>(reactome, BioSystems)","Role of nicotinic acetylcholine receptors in the regulation of apoptosis<br/>(biocarta, BioCarta)","Interactions of Rev with host cellular proteins<br/>(reactome, BioSystems)","Arachidonate Epoxygenase / Epoxide Hydrolase<br/>(wiki, BioSystems)","spermine and spermidine degradation I<br/>(biocyc, BioSystems)"],[6,9,11,12,2,3,2,12,12,2,8,9,62,4,4,21,3,3,4,3,3,3,2,3,3,2,2,3,4,2,3,2,10,21,2,2,3,2,3,8,2,2,3,2,2,4,4,2,154,157,3,149,56,2,3,2,9,11,11,7,9,11,12,10,8,11,14,11,10,26,11,18,41,74,190,18,32,126,127,30,14,18,40,41,122,49,50,61,45,47,48,31,44,49,33,32,16,34,7,3],[480,378,1025,925,163,285,143,1104,1197,233,652,803,6029,290,331,1931,133,197,257,246,280,286,127,160,312,180,204,182,313,150,350,186,979,2396,96,175,176,138,200,663,150,221,147,122,261,435,201,201,14212,14466,230,13486,4984,172,248,122,1715,1281,928,563,1642,962,1122,2101,702,1113,3028,2376,815,3188,971,1366,7347,2908,19483,3690,5513,19033,19033,4629,1504,1964,930,930,18540,1207,1207,7181,3655,3143,3148,2699,3095,3509,2855,2794,1814,2950,643,192],[190.349225776758,168.864176219219,130.857552651858,116.175146825028,96.8615214900348,83.7583629004608,79.9990793618097,78.0109715609269,55.2543673893159,47.6533779896539,42.2292397284462,42.067167334342,40.7604299580373,35.5760235609061,32.3720480960201,31.7733760671916,31.1330744678135,29.9698516978958,27.3405133763317,23.1367038708271,22.5673786742413,21.3295494739836,20.3173781530275,19.4752059294431,18.8876780081182,18.6511333404338,18.2497591058326,16.9960849519533,15.6818259539155,14.9236258717373,14.0822638067041,14.01425859495,11.0580926101448,10.5945728160063,9.95054166406813,9.23689416202616,8.21271523653057,8.11111741728113,8.03255634670328,8.02853848577014,7.81286034579526,7.35772872452721,6.9693593100872,6.75083279625696,6.46416090556408,4.69503563430814,4.2571375140471,3.66092419385686,3.08538126483387,3.03674146082706,2.77819873656626,2.66042687475542,2.02774748218552,1.89916910134435,1.89269017146282,1.77770742573459,1.68982880676351,1.61210530643021,1.6067032246408,1.60658011822186,1.5744914015217,1.55388519935816,1.54717219728066,1.52257432682908,1.51416174188173,1.51272725376139,1.49496827897905,1.45126340016639,1.44902049623767,1.44232345420426,1.43377440417223,1.36939622639712,1.30742349423208,1.2569996472916,1.25666861401583,1.23858413593948,1.22141206301524,1.22042620737607,1.22042620737607,1.20602468007555,1.19316615282112,1.08083225861214,1.07977085280249,1.07977085280249,1.05762398463543,1.01021709245082,1.01021709245082,0.955711949996216,0.92562454405279,0.873643378327604,0.872147979552199,0.834906430605899,0.828764169438142,0.826255102546295,0.817640962796467,0.808581236321452,0.800118500776996,0.792209796852266,-0.249563577614721,-0.336184446167102],["-4.2692<br/>[-4.4624, 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-4.1748]","-4.2768<br/>[-4.4741, -4.1765]","-4.2690<br/>[-4.4622, -4.1702]","-4.2745<br/>[-4.4732, -4.1748]","-4.2764<br/>[-4.4737, -4.1760]","-4.2690<br/>[-4.4622, -4.1701]","-4.2746<br/>[-4.4734, -4.1749]","-4.2744<br/>[-4.4731, -4.1747]","-4.2764<br/>[-4.4737, -4.1760]","-4.2750<br/>[-4.4736, -4.1753]","-4.2764<br/>[-4.4737, -4.1760]","-4.2770<br/>[-4.4661, -4.1774]","-4.2761<br/>[-4.4741, -4.1766]","-4.2772<br/>[-4.4741, -4.1769]","-4.2719<br/>[-4.4696, -4.1729]","-4.2740<br/>[-4.4726, -4.1744]","-4.2743<br/>[-4.4728, -4.1747]","-4.2717<br/>[-4.4694, -4.1727]","-4.2717<br/>[-4.4694, -4.1727]","-4.2741<br/>[-4.4726, -4.1745]","-4.2761<br/>[-4.4734, -4.1758]","-4.2760<br/>[-4.4733, -4.1757]","-4.2695<br/>[-4.4626, -4.1706]","-4.2695<br/>[-4.4626, -4.1706]","-4.2745<br/>[-4.4719, -4.1754]","-4.2694<br/>[-4.4625, -4.1705]","-4.2694<br/>[-4.4625, -4.1705]","-4.2731<br/>[-4.4716, -4.1736]","-4.2696<br/>[-4.4636, -4.1710]","-4.2768<br/>[-4.4657, -4.1772]","-4.2768<br/>[-4.4657, -4.1772]","-4.2698<br/>[-4.4638, -4.1711]","-4.2767<br/>[-4.4656, -4.1771]","-4.2768<br/>[-4.4656, -4.1773]","-4.2698<br/>[-4.4638, -4.1711]","-4.2697<br/>[-4.4638, -4.1711]","-4.2751<br/>[-4.4650, -4.1754]","-4.2697<br/>[-4.4637, -4.1711]","-4.2699<br/>[-4.4629, -4.1711]","-4.2693<br/>[-4.4625, -4.1704]"],["-1.3766<br/>[-1.3766, -1.3761]","-1.6503<br/>[-1.6535, -1.6442]","-1.5698<br/>[-1.5699, -1.5696]","-1.6727<br/>[-1.6727, -1.6727]","-1.2920<br/>[-1.2936, -1.2864]","-2.1407<br/>[-2.1534, -2.1240]","-1.3538<br/>[-1.3683, -1.3366]","-1.5924<br/>[-1.5924, -1.5922]","-2.4000<br/>[-2.4682, -2.3483]","-1.8589<br/>[-1.8860, -1.8277]","-2.4608<br/>[-2.5059, -2.4137]","-2.5431<br/>[-2.5955, -2.4851]","-3.3638<br/>[-3.4490, -3.2488]","-2.1241<br/>[-2.1596, -2.0843]","-2.1786<br/>[-2.2158, -2.1291]","-2.5948<br/>[-2.6661, -2.5377]","-1.5039<br/>[-1.5190, -1.4888]","-1.9610<br/>[-1.9902, -1.9193]","-1.7776<br/>[-1.8006, -1.7467]","-1.9471<br/>[-2.0684, -1.8334]","-2.1151<br/>[-2.1439, -2.0759]","-2.1188<br/>[-2.1529, -2.0728]","-1.4765<br/>[-1.4978, -1.4563]","-1.7079<br/>[-1.7242, -1.6873]","-2.1656<br/>[-2.1909, -2.1302]","-1.9158<br/>[-1.9517, -1.8700]","-1.9797<br/>[-2.0066, -1.9458]","-1.6082<br/>[-1.6475, -1.5670]","-2.0272<br/>[-2.1438, -1.9354]","-1.3661<br/>[-1.3867, -1.3416]","-2.1959<br/>[-2.2404, -2.1442]","-1.7433<br/>[-1.7809, -1.7091]","-2.8820<br/>[-2.9804, -2.7525]","-2.7213<br/>[-2.7230, -2.7174]","-1.5980<br/>[-1.6660, -1.5323]","-1.9172<br/>[-1.9408, -1.8825]","-1.9031<br/>[-1.9420, -1.8599]","-1.8195<br/>[-1.8385, -1.7947]","-1.7432<br/>[-1.8235, -1.7051]","-2.4724<br/>[-2.5186, -2.4132]","-1.8524<br/>[-1.8748, -1.8240]","-1.8238<br/>[-1.8626, -1.7804]","-1.8194<br/>[-1.8619, -1.7687]","-1.7496<br/>[-1.7835, -1.7037]","-2.0700<br/>[-2.1127, -2.0183]","-2.0044<br/>[-2.0570, -1.9507]","-1.9543<br/>[-2.0000, -1.8986]","-1.9454<br/>[-2.0001, -1.8873]","-3.2101<br/>[-3.3869, -3.0924]","-3.2201<br/>[-3.3941, -3.1003]","-1.9740<br/>[-2.0571, -1.8911]","-3.2366<br/>[-3.3991, -3.1223]","-3.1289<br/>[-3.3109, -3.0073]","-1.9140<br/>[-1.9337, -1.8867]","-1.8861<br/>[-1.9156, -1.8529]","-1.5397<br/>[-1.6058, -1.4744]","-3.0192<br/>[-3.2077, -2.8262]","-2.8467<br/>[-3.0678, -2.7177]","-2.9079<br/>[-2.9652, -2.8094]","-2.7056<br/>[-2.7493, -2.6303]","-3.1027<br/>[-3.2081, -2.9600]","-2.8264<br/>[-2.9478, -2.6989]","-2.9714<br/>[-3.0462, -2.8630]","-3.1546<br/>[-3.3102, -2.9784]","-2.7976<br/>[-2.8445, -2.7135]","-3.0018<br/>[-3.0458, -2.9289]","-3.2106<br/>[-3.4280, -3.0241]","-3.2222<br/>[-3.3598, -3.0442]","-2.8624<br/>[-2.9092, -2.7805]","-3.2634<br/>[-3.4410, -3.0807]","-2.8850<br/>[-2.9832, -2.7569]","-2.7745<br/>[-2.9332, -2.6478]","-3.4551<br/>[-3.6726, -3.2745]","-3.1520<br/>[-3.3918, -2.9792]","-3.7198<br/>[-3.9004, -3.5576]","-3.4274<br/>[-3.5495, -3.2750]","-3.4523<br/>[-3.6610, -3.2447]","-3.7414<br/>[-3.8836, -3.5783]","-3.7414<br/>[-3.8836, -3.5783]","-3.4616<br/>[-3.6235, -3.2793]","-3.1178<br/>[-3.1740, -3.0304]","-3.2284<br/>[-3.2891, -3.1357]","-2.9075<br/>[-2.9650, -2.8219]","-2.9075<br/>[-2.9650, -2.8219]","-3.8042<br/>[-4.0445, -3.5993]","-3.0240<br/>[-3.0773, -2.9397]","-3.0240<br/>[-3.0773, -2.9397]","-3.6931<br/>[-3.8221, -3.5393]","-3.0908<br/>[-3.4462, -2.8624]","-3.0836<br/>[-3.3250, -2.9170]","-3.0845<br/>[-3.3262, -2.9180]","-3.1146<br/>[-3.3785, -2.9549]","-3.1077<br/>[-3.3431, -2.9610]","-3.1171<br/>[-3.3748, -2.9448]","-3.1287<br/>[-3.3919, -2.9577]","-3.1335<br/>[-3.3853, -2.9683]","-2.9863<br/>[-3.2316, -2.8250]","-3.1469<br/>[-3.4285, -2.9832]","-3.0627<br/>[-4.1493, -2.7545]","-3.6543<br/>[-5.3975, -3.0410]"]],"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":[["Thyroid","Brain - Cerebellum","Brain - Cerebellar Hemisphere","Heart - Atrial Appendage","Brain - Hippocampus","Brain - Anterior cingulate cortex (BA24)","Brain - Cortex","Brain - Nucleus accumbens (basal ganglia)","Brain - Frontal Cortex (BA9)","Brain - Caudate (basal ganglia)","Brain - Hypothalamus","Brain - Putamen (basal ganglia)","Adrenal Gland","Cells - EBV-transformed lymphocytes","Pituitary","Liver","Muscle - Skeletal","Heart - Left Ventricle","Whole Blood","Spleen","Esophagus - Mucosa","Vagina","Small Intestine - Terminal Ileum","Lung","Colon - Transverse","Pancreas","Esophagus - Gastroesophageal Junction","Stomach","Ovary","Colon - Sigmoid","Uterus","Esophagus - Muscularis","Artery - Tibial","Cells - Transformed fibroblasts","Prostate","Testis","Breast - Mammary Tissue","Nerve - Tibial","Adipose - Visceral (Omentum)","Adipose - Subcutaneous","Skin - Not Sun Exposed (Suprapubic)","Skin - Sun Exposed (Lower leg)","Artery - Coronary","Artery - Aorta"],[6915,6553,6396,6701,6531,6703,6666,6862,6930,7294,6566,7369,6416,5602,6617,7023,6461,6442,6613,4664,6242,6483,5317,5614,5908,5782,6485,5958,6682,6604,6420,6695,6720,6797,6359,6805,6341,6436,6586,6374,6607,6522,6891,7004],[0.509008764346557,0.473190757900193,0.472945182481959,0.259296193450623,0.155902038689513,0.131310368397108,0.127078922752595,0.101977078261649,0.0913210315802674,0.0571382140618579,0.0552493911442937,0.0520563723667016,-0.156080285612782,-0.168192941126796,-0.24491592813199,-0.246886555998921,-0.384941590273925,-0.452359130049513,-0.461306420969293,-0.527583085208731,-0.552634019159298,-0.559849533831099,-0.564678576065957,-0.567291462437769,-0.570702460576614,-0.579075853244744,-0.587810228717329,-0.590054175456487,-0.591389286678712,-0.592162700156783,-0.594877118434499,-0.59615460271647,-0.599264521917624,-0.603020876808734,-0.603312173626027,-0.60500391027972,-0.60514177046508,-0.607142717762225,-0.607250294679058,-0.608231321001344,-0.612181875468851,-0.613984892758948,-0.617772118240034,-0.627828074677366],["-4.2814<br/>[-4.4808, -4.1800]","-4.2747<br/>[-4.4698, -4.1750]","-4.2747<br/>[-4.4698, -4.1750]","-4.2731<br/>[-4.4623, -4.1735]","-4.2771<br/>[-4.4711, -4.1776]","-4.2770<br/>[-4.4710, -4.1776]","-4.2770<br/>[-4.4710, -4.1775]","-4.2770<br/>[-4.4709, -4.1775]","-4.2769<br/>[-4.4709, -4.1774]","-4.2768<br/>[-4.4708, -4.1774]","-4.2766<br/>[-4.4707, -4.1770]","-4.2768<br/>[-4.4708, -4.1774]","-4.2747<br/>[-4.4699, -4.1749]","-4.2743<br/>[-4.4696, -4.1745]","-4.2740<br/>[-4.4692, -4.1742]","-4.2741<br/>[-4.4692, -4.1743]","-4.2705<br/>[-4.4622, -4.1720]","-4.2733<br/>[-4.4625, -4.1736]","-4.2734<br/>[-4.4625, -4.1737]","-4.2682<br/>[-4.4612, -4.1694]","-4.2682<br/>[-4.4611, -4.1694]","-4.2681<br/>[-4.4611, -4.1693]","-4.2680<br/>[-4.4609, -4.1692]","-4.2680<br/>[-4.4609, -4.1692]","-4.2680<br/>[-4.4609, -4.1693]","-4.2679<br/>[-4.4608, -4.1691]","-4.2679<br/>[-4.4608, -4.1692]","-4.2678<br/>[-4.4607, -4.1690]","-4.2680<br/>[-4.4608, -4.1693]","-4.2679<br/>[-4.4607, -4.1692]","-4.2678<br/>[-4.4607, -4.1691]","-4.2679<br/>[-4.4607, -4.1692]","-4.2678<br/>[-4.4607, -4.1691]","-4.2678<br/>[-4.4606, -4.1691]","-4.2677<br/>[-4.4606, -4.1689]","-4.2678<br/>[-4.4606, -4.1691]","-4.2677<br/>[-4.4606, -4.1689]","-4.2677<br/>[-4.4606, -4.1689]","-4.2677<br/>[-4.4606, -4.1690]","-4.2676<br/>[-4.4606, -4.1689]","-4.2676<br/>[-4.4605, -4.1689]","-4.2676<br/>[-4.4605, -4.1688]","-4.2676<br/>[-4.4605, -4.1689]","-4.2675<br/>[-4.4604, -4.1688]"],["-3.4536<br/>[-3.5778, -3.3159]","-3.3607<br/>[-3.5105, -3.2201]","-3.3604<br/>[-3.5021, -3.2262]","-3.6777<br/>[-3.8178, -3.5126]","-3.4149<br/>[-3.7012, -3.2198]","-3.4317<br/>[-3.7049, -3.2344]","-3.4344<br/>[-3.7039, -3.2398]","-3.4523<br/>[-3.7238, -3.2614]","-3.4594<br/>[-3.7240, -3.2656]","-3.4834<br/>[-3.7663, -3.2945]","-3.4788<br/>[-3.7214, -3.2944]","-3.4869<br/>[-3.7450, -3.2882]","-3.6146<br/>[-3.8271, -3.4276]","-3.6238<br/>[-3.8066, -3.4580]","-3.6988<br/>[-3.8764, -3.5365]","-3.6964<br/>[-3.9047, -3.5237]","-3.7717<br/>[-4.5316, -3.4903]","-3.6660<br/>[-3.8916, -3.4550]","-3.6750<br/>[-3.9151, -3.4710]","-4.2582<br/>[-5.1168, -3.8541]","-4.1639<br/>[-4.7467, -3.8495]","-4.1653<br/>[-4.7296, -3.8449]","-4.3490<br/>[-5.1759, -3.9571]","-4.2975<br/>[-5.1587, -3.9110]","-4.2630<br/>[-5.0730, -3.8830]","-4.3385<br/>[-5.1524, -3.9545]","-4.2626<br/>[-5.0606, -3.8900]","-4.3727<br/>[-5.1843, -3.9909]","-4.2624<br/>[-5.0000, -3.9124]","-4.2675<br/>[-5.0630, -3.8941]","-4.3124<br/>[-5.1044, -3.9385]","-4.2751<br/>[-5.1035, -3.9047]","-4.2877<br/>[-5.1144, -3.9198]","-4.2965<br/>[-5.0899, -3.9289]","-4.3757<br/>[-5.1755, -3.9986]","-4.3040<br/>[-5.1044, -3.9310]","-4.3922<br/>[-5.1937, -4.0160]","-4.3849<br/>[-5.1677, -4.0061]","-4.3542<br/>[-5.1401, -3.9747]","-4.4075<br/>[-5.2221, -4.0321]","-4.3832<br/>[-5.1829, -4.0061]","-4.4155<br/>[-5.2267, -4.0416]","-4.3657<br/>[-5.1575, -3.9965]","-4.4111<br/>[-5.1941, -4.0428]"]],"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":[["Brain_Cortex","Muscle_Skeletal","Pituitary","Ovary","Spleen","Testis","Cells_EBV-transformed_lymphocytes","Artery_Coronary","Cells_Transformed_fibroblasts","Adipose_Subcutaneous","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Brain_Putamen_(basal_ganglia)","Brain_Cerebellum","Whole_Blood","Colon_Sigmoid","Nerve_Tibial","Stomach","Esophagus_Mucosa","Vagina","Kidney_Cortex","Pancreas","Colon_Transverse","Liver","Prostate","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Cerebellar_Hemisphere","Thyroid","Lung","Brain_Hippocampus","Brain_Frontal_Cortex_(BA9)","Minor_Salivary_Gland","Small_Intestine_Terminal_Ileum","Breast_Mammary_Tissue","Adipose_Visceral_(Omentum)","Brain_Amygdala","Adrenal_Gland","Brain_Caudate_(basal_ganglia)","Brain_Nucleus_accumbens_(basal_ganglia)","Artery_Tibial","Heart_Left_Ventricle","Brain_Hypothalamus","Uterus","Heart_Atrial_Appendage","Brain_Substantia_nigra","Esophagus_Muscularis","Artery_Aorta","Esophagus_Gastroesophageal_Junction","Brain_Spinal_cord_(cervical_c-1)"],[12762,9430,10359,12345,7901,8424,8421,13113,11219,10831,7322,7386,12570,11728,7914,11586,13281,10053,7437,7317,9629,8210,8353,8933,9851,13908,14304,12787,9031,11879,14418,9184,9523,10533,10629,12068,13120,12446,12202,13231,11688,13013,13203,11778,13455,14843,15021,14710,13381],[26.2682835462304,0.440210229776548,0.195533946068141,-0.0692352647568092,-0.178378532946302,-0.302717506679789,-0.316706636465756,-0.42004285071152,-0.445144256131623,-0.458797179637458,-0.486634668715401,-0.489021103826243,-0.489525115031453,-0.50029560071075,-0.515189226552765,-0.520366732027974,-0.52417892816938,-0.588506546659588,-0.607037275220108,-0.610826440394464,-0.633710763763505,-0.633827024005665,-0.658042997473194,-0.665942173526448,-0.671706040475893,-0.680852369778795,-0.687828253393475,-0.689275608454174,-0.693483830088707,-0.694891493789519,-0.698479621262007,-0.704329787948761,-0.714311138341079,-0.728635748077478,-0.732711682692343,-0.73442253656811,-0.736705800181701,-0.737937726169591,-0.739243839944154,-0.739780578114741,-0.744159921043038,-0.75607129045518,-0.763228583334143,-0.764066083729213,-0.775016886647212,-0.778716135009356,-0.789870964295002,-0.792127224388626,-0.793730137859334],["-4.2745<br/>[-4.4709, -4.1745]","-4.2756<br/>[-4.4639, -4.1763]","-4.2814<br/>[-4.4816, -4.1800]","-4.2733<br/>[-4.4702, -4.1732]","-4.2683<br/>[-4.4611, -4.1696]","-4.2731<br/>[-4.4666, -4.1739]","-4.2667<br/>[-4.4597, -4.1680]","-4.2740<br/>[-4.4706, -4.1740]","-4.2666<br/>[-4.4593, -4.1680]","-4.2663<br/>[-4.4599, -4.1676]","-4.2699<br/>[-4.4622, -4.1713]","-4.2698<br/>[-4.4622, -4.1713]","-4.2732<br/>[-4.4694, -4.1732]","-4.2707<br/>[-4.4623, -4.1725]","-4.2733<br/>[-4.4623, -4.1737]","-4.2716<br/>[-4.4649, -4.1725]","-4.2720<br/>[-4.4650, -4.1729]","-4.2692<br/>[-4.4614, -4.1707]","-4.2677<br/>[-4.4607, -4.1690]","-4.2677<br/>[-4.4606, -4.1689]","-4.2674<br/>[-4.4602, -4.1688]","-4.2672<br/>[-4.4601, -4.1685]","-4.2673<br/>[-4.4601, -4.1687]","-4.2673<br/>[-4.4599, -4.1686]","-4.2673<br/>[-4.4599, -4.1687]","-4.2675<br/>[-4.4597, -4.1692]","-4.2681<br/>[-4.4600, -4.1699]","-4.2679<br/>[-4.4605, -4.1695]","-4.2669<br/>[-4.4598, -4.1682]","-4.2674<br/>[-4.4597, -4.1690]","-4.2673<br/>[-4.4595, -4.1689]","-4.2667<br/>[-4.4596, -4.1680]","-4.2666<br/>[-4.4595, -4.1679]","-4.2664<br/>[-4.4592, -4.1678]","-4.2664<br/>[-4.4592, -4.1677]","-4.2667<br/>[-4.4592, -4.1682]","-4.2670<br/>[-4.4593, -4.1685]","-4.2668<br/>[-4.4593, -4.1683]","-4.2666<br/>[-4.4591, -4.1681]","-4.2670<br/>[-4.4594, -4.1685]","-4.2715<br/>[-4.4606, -4.1719]","-4.2665<br/>[-4.4589, -4.1680]","-4.2663<br/>[-4.4588, -4.1678]","-4.2713<br/>[-4.4604, -4.1716]","-4.2662<br/>[-4.4586, -4.1677]","-4.2663<br/>[-4.4585, -4.1678]","-4.2658<br/>[-4.4583, -4.1672]","-4.2660<br/>[-4.4583, -4.1675]","-4.2657<br/>[-4.4583, -4.1672]"],["-3.0701<br/>[-3.0786, -3.0523]","-3.5525<br/>[-3.7999, -3.3591]","-3.5270<br/>[-3.6952, -3.3881]","-3.6782<br/>[-3.7796, -3.5720]","-3.6566<br/>[-3.8340, -3.4906]","-3.7123<br/>[-4.0846, -3.4745]","-3.7862<br/>[-3.8933, -3.6704]","-3.8537<br/>[-4.0457, -3.6649]","-3.8889<br/>[-4.0607, -3.7377]","-3.9096<br/>[-4.0550, -3.7666]","-3.9371<br/>[-4.5203, -3.6696]","-3.9395<br/>[-4.5228, -3.6708]","-3.9280<br/>[-4.0923, -3.7752]","-3.8702<br/>[-4.4819, -3.5784]","-3.7225<br/>[-3.9634, -3.5025]","-3.9502<br/>[-4.2818, -3.7617]","-3.9343<br/>[-4.2827, -3.7289]","-4.0555<br/>[-4.6199, -3.7819]","-4.2594<br/>[-4.8152, -3.9554]","-4.2889<br/>[-4.8388, -3.9831]","-4.1571<br/>[-4.8158, -3.8037]","-4.2701<br/>[-4.9694, -3.9134]","-4.3705<br/>[-5.1340, -4.0067]","-4.3448<br/>[-5.0875, -4.0041]","-4.2796<br/>[-4.9883, -3.9355]","-4.1160<br/>[-4.7527, -3.7943]","-4.1257<br/>[-4.8007, -3.8173]","-4.1890<br/>[-4.7200, -3.9096]","-4.4947<br/>[-5.1988, -4.1552]","-4.2318<br/>[-4.9355, -3.9054]","-4.1424<br/>[-4.7993, -3.8295]","-4.5403<br/>[-5.3081, -4.1869]","-4.5543<br/>[-5.3532, -4.2031]","-4.4975<br/>[-5.2098, -4.1693]","-4.5107<br/>[-5.2201, -4.1831]","-4.3657<br/>[-5.0761, -4.0390]","-4.3115<br/>[-4.9388, -4.0107]","-4.3562<br/>[-5.0207, -4.0446]","-4.3762<br/>[-5.0936, -4.0521]","-4.3189<br/>[-4.9218, -4.0262]","-3.9680<br/>[-4.1653, -3.7842]","-4.3894<br/>[-5.0867, -4.0756]","-4.4067<br/>[-5.0964, -4.0949]","-3.9988<br/>[-4.1825, -3.8299]","-4.4422<br/>[-5.1437, -4.1308]","-4.3618<br/>[-5.0558, -4.0588]","-4.4066<br/>[-4.9638, -4.1366]","-4.4256<br/>[-5.0654, -4.1153]","-4.5520<br/>[-5.2282, -4.2318]"]],"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":[["8","1","19","12","7","6","9","11","17","14","2","13","15","16","18","10","20","5","4","3"],[10756,8494,6540,7719,9062,9648,10233,11104,9334,10063,10153,8478,8556,10894,7965,9213,8977,12195,12972,10847],[1.28631191195372,0.199788150897773,-0.178177255441324,-0.182862409120457,-0.46905219772038,-0.519426820509027,-0.541266370851156,-0.595446272819743,-0.601022453277084,-0.637991464660879,-0.643723892013679,-0.645799647947085,-0.646322943225992,-0.647411343483802,-0.66647461765959,-0.67274255919081,-0.684728221571923,-0.719517039546496,-0.725134789560204,-0.749978682843429],["-4.2753<br/>[-4.4718, -4.1753]","-4.2682<br/>[-4.4624, -4.1694]","-4.2679<br/>[-4.4608, -4.1692]","-4.2748<br/>[-4.4698, -4.1752]","-4.2704<br/>[-4.4620, -4.1721]","-4.2675<br/>[-4.4603, -4.1688]","-4.2698<br/>[-4.4613, -4.1715]","-4.2687<br/>[-4.4614, -4.1700]","-4.2728<br/>[-4.4618, -4.1732]","-4.2723<br/>[-4.4613, -4.1727]","-4.2670<br/>[-4.4597, -4.1684]","-4.2675<br/>[-4.4605, -4.1688]","-4.2674<br/>[-4.4603, -4.1687]","-4.2682<br/>[-4.4608, -4.1695]","-4.2672<br/>[-4.4600, -4.1684]","-4.2674<br/>[-4.4602, -4.1687]","-4.2671<br/>[-4.4600, -4.1684]","-4.2668<br/>[-4.4595, -4.1682]","-4.2672<br/>[-4.4597, -4.1687]","-4.2662<br/>[-4.4590, -4.1675]"],["-3.5248<br/>[-3.7032, -3.3773]","-3.6366<br/>[-3.8631, -3.4184]","-3.6313<br/>[-3.8575, -3.4471]","-3.6339<br/>[-3.9054, -3.4338]","-3.8639<br/>[-4.5281, -3.5900]","-3.9090<br/>[-4.5036, -3.5180]","-3.9544<br/>[-4.6543, -3.6782]","-4.0249<br/>[-4.6101, -3.7155]","-3.8099<br/>[-4.0399, -3.6030]","-3.8461<br/>[-4.0734, -3.6407]","-4.1858<br/>[-4.7230, -3.9099]","-4.3038<br/>[-4.9186, -3.9261]","-4.3121<br/>[-4.8611, -4.0125]","-4.1533<br/>[-4.7011, -3.8236]","-4.4947<br/>[-5.2858, -4.1397]","-4.3580<br/>[-4.9940, -4.0476]","-4.4535<br/>[-5.0763, -4.1368]","-4.3172<br/>[-4.8384, -4.0447]","-4.2825<br/>[-4.8574, -3.9826]","-4.5991<br/>[-5.3300, -4.2632]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Cluster ID<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
<p>The relationship between tissues and clusters is shown in Figure 1 of <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006599">Dey et al. (2017)</a>; see below.</p>
<p><img src="http://journals.plos.org/plosgenetics/article/figure/image?size=large&id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.4 plyr_1.8.4 dplyr_0.7.5 R.matlab_3.6.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 compiler_3.5.0 pillar_1.2.3
[4] later_0.7.3 git2r_0.21.0 workflowr_1.0.1
[7] bindr_0.1.1 R.methodsS3_1.7.1 R.utils_2.6.0
[10] tools_3.5.0 digest_0.6.15 jsonlite_1.5
[13] evaluate_0.10.1 tibble_1.4.2 pkgconfig_2.0.1
[16] rlang_0.2.1 shiny_1.1.0 crosstalk_1.0.0
[19] yaml_2.1.19 bindrcpp_0.2.2 stringr_1.3.1
[22] knitr_1.20 htmlwidgets_1.2 rprojroot_1.3-2
[25] tidyselect_0.2.4 glue_1.2.0 R6_2.2.2
[28] rmarkdown_1.10 purrr_0.2.5 magrittr_1.5
[31] whisker_0.3-2 backports_1.1.2 promises_1.0.1
[34] htmltools_0.3.6 assertthat_0.2.0 mime_0.5
[37] xtable_1.8-2 httpuv_1.4.4.1 stringi_1.2.3
[40] R.oo_1.22.0 </code></pre>
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