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<h1 class="title toc-ignore">Enrichment results of total cholesterol</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> 2018-07-02</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/20686565">“Biological, Clinical and Population Relevance of 95 Loci for Blood Lipids” (<em>Nature</em>, 2010)</a>. The summary data file is available at <a href="http://csg.sph.umich.edu/willer/public/lipids2010" class="uri">http://csg.sph.umich.edu/willer/public/lipids2010</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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PC)","Norepinephrine Neurotransmitter Release Cycle<br/>(reactome, PC)","Endocytosis<br/>(kegg, BioSystems)","Na+/Cl- dependent neurotransmitter transporters<br/>(reactome, PC)","Neurotransmitter Release Cycle<br/>(reactome, PC)","Selenium Pathway<br/>(wiki, BioSystems)","Neurotransmitter Release Cycle<br/>(reactome, BioSystems)","Organic cation transport<br/>(reactome, BioSystems)","Cohesin Loading onto Chromatin<br/>(reactome, BioSystems)","Adherens junctions interactions<br/>(reactome, PC)","Fat digestion and absorption<br/>(kegg, BioSystems)","Orphan transporters<br/>(reactome, PC)","Transmission across Chemical Synapses<br/>(reactome, BioSystems)","Cell-cell junction organization<br/>(reactome, PC)","Cell adhesion molecules (CAMs)<br/>(kegg, BioSystems)","Electron Transport Chain<br/>(wiki, BioSystems)","Cell junction organization<br/>(reactome, PC)","Cell junction organization<br/>(reactome, BioSystems)","Cell-Cell communication<br/>(reactome, PC)","Cell-Cell communication<br/>(reactome, BioSystems)","Herpes simplex infection<br/>(kegg, BioSystems)","TNF-alpha/NF-kB Signaling Pathway<br/>(wiki, BioSystems)","Neuronal System<br/>(reactome, PC)","Chronic myeloid leukemia<br/>(kegg, BioSystems)","Scavenging by Class B Receptors<br/>(reactome, PC)","Mitochondrial protein import<br/>(reactome, PC)","Monoamine Transport<br/>(wiki, BioSystems)","LKB1 signaling events<br/>(pid, PC)","Chromatin modifying enzymes<br/>(reactome, PC)","Chromatin modifying enzymes<br/>(reactome, BioSystems)","SLC-mediated transmembrane transport<br/>(reactome, BioSystems)","Metabolism of carbohydrates<br/>(reactome, BioSystems)","SLC-mediated transmembrane transport<br/>(reactome, PC)","HATs acetylate histones<br/>(reactome, PC)","HATs acetylate histones<br/>(reactome, BioSystems)","Carbohydrate metabolism<br/>(reactome, PC)","Hexose transport<br/>(reactome, BioSystems)","Glucose transport<br/>(reactome, PC)","Hexose uptake<br/>(reactome, PC)"],[22,25,41,28,29,5,5,4,8,14,9,6,26,30,50,58,30,2,3,2,4,3,17,10,14,15,5,7,231,40,41,39,40,13,157,88,89,15,19,19,7,174,181,107,109,110,112,25,6,169,77,30,72,69,6,8,23,93,20,14,18,29,17,252,18,40,85,47,9,8,30,41,96,200,59,134,87,82,83,126,127,174,181,269,71,5,47,31,42,203,241,254,253,251,132,136,244,47,39,45],[1717,1937,3156,2120,2207,489,390,543,906,1372,1009,486,2905,2314,3969,4473,2625,153,217,262,281,305,1140,1026,1403,1472,613,673,19684,4183,4243,4555,4555,1027,14683,8940,8940,1467,2347,1509,666,17117,17676,11219,11318,11527,11626,2900,512,15665,9557,3423,4868,3451,452,841,2937,4510,1668,1277,2343,3166,2034,22230,1854,4661,6872,5499,1091,721,5592,2638,8649,24018,8024,14598,5809,10577,10577,17250,17250,10810,14429,32090,6438,506,3298,2992,3591,11667,15124,23944,23181,23473,5705,6107,22614,3645,3001,3490],[1046.71297038265,1030.28057706807,833.167736335236,833.115109164907,833.071238617996,189.412834516806,177.78667497423,177.606383982322,176.519771704914,176.513044553226,176.423292674786,136.651722355881,135.600403658823,127.100950038157,122.69621790464,120.46859127399,117.920825753058,107.296825018183,107.009357779274,106.830601775116,106.783206225496,106.694501749244,105.44046429875,92.7095375729518,92.4177766411033,92.306490486481,91.7966797796013,82.9032332225167,65.8193195674651,65.7480962726918,65.4064751492399,64.6114076553592,64.6114076553592,63.0634896671963,62.2600756659802,60.0740049626721,60.0740049626721,59.8517866692081,57.9973025606874,56.8794544735574,48.2210247522355,45.2811871416823,44.8074170145675,43.8792314614443,43.7693079329668,43.7680415185022,43.6785397232853,42.7157227956977,42.5213265472326,42.4481937268736,42.3689586787171,41.3946922430321,40.6150444093429,40.4683606234445,39.483711575291,38.4208985755171,38.0521436936433,38.0239488153225,37.5638421585216,37.4438464769592,37.0535321876074,36.6888290432167,36.626335263684,36.1917445663657,36.0239955426929,35.5570001462603,35.007134320934,34.8192630174718,34.2823940652204,34.2108113389209,33.4222511081726,33.2861119387045,32.8412258368669,32.3963908078288,32.2865546596225,31.5848750803951,31.2203209780455,30.9615949836417,30.9615949836417,30.8411480412691,30.8411480412691,29.456792792058,29.3813293082727,29.0392145240454,28.2441535165126,27.8424633252401,27.4933984572174,27.0280169769773,26.5944645829211,11.5055797344586,10.5202917192331,4.5808792825295,3.63777074909445,3.41635699391635,3.23941239555911,3.12340305431543,2.58855473113178,2.1802497234865,0.980640425662793,0.86097385271057],["-4.0271<br/>[-4.0397, -4.0140]","-4.0270<br/>[-4.0396, -4.0139]","-4.0354<br/>[-4.0481, -4.0223]","-4.0314<br/>[-4.0442, -4.0182]","-4.0314<br/>[-4.0441, -4.0182]","-4.0275<br/>[-4.0402, -4.0144]","-4.0308<br/>[-4.0434, -4.0178]","-4.0287<br/>[-4.0413, -4.0158]","-4.0285<br/>[-4.0410, -4.0155]","-4.0287<br/>[-4.0412, -4.0158]","-4.0284<br/>[-4.0410, -4.0155]","-4.0366<br/>[-4.0495, -4.0233]","-4.0416<br/>[-4.0545, -4.0283]","-4.2045<br/>[-4.2202, -4.1886]","-4.2140<br/>[-4.2294, -4.1983]","-4.2138<br/>[-4.2292, -4.1981]","-4.1939<br/>[-4.2088, -4.1788]","-4.0277<br/>[-4.0403, -4.0146]","-4.0276<br/>[-4.0403, -4.0145]","-4.0276<br/>[-4.0403, -4.0145]","-4.0276<br/>[-4.0402, -4.0145]","-4.0276<br/>[-4.0402, -4.0145]","-4.1559<br/>[-4.1697, -4.1419]","-4.0410<br/>[-4.0540, -4.0275]","-4.0272<br/>[-4.0398, -4.0141]","-4.0271<br/>[-4.0398, -4.0141]","-4.0411<br/>[-4.0542, -4.0276]","-4.0365<br/>[-4.0494, -4.0232]","-4.1290<br/>[-4.1404, -4.1176]","-4.1093<br/>[-4.1212, -4.0974]","-4.1093<br/>[-4.1212, -4.0973]","-4.1368<br/>[-4.1500, -4.1233]","-4.1368<br/>[-4.1500, -4.1233]","-4.0410<br/>[-4.0540, -4.0275]","-4.0649<br/>[-4.0786, -4.0507]","-4.1353<br/>[-4.1485, -4.1219]","-4.1353<br/>[-4.1485, -4.1219]","-4.1054<br/>[-4.1201, -4.0902]","-4.1019<br/>[-4.1144, -4.0891]","-4.0943<br/>[-4.1087, -4.0793]","-4.0765<br/>[-4.0903, -4.0623]","-4.0899<br/>[-4.1041, -4.0752]","-4.0897<br/>[-4.1039, -4.0750]","-4.0869<br/>[-4.1010, -4.0723]","-4.0868<br/>[-4.1010, -4.0722]","-4.0868<br/>[-4.1009, -4.0722]","-4.0867<br/>[-4.1008, -4.0721]","-4.0784<br/>[-4.0918, -4.0644]","-4.0878<br/>[-4.1001, -4.0752]","-4.1092<br/>[-4.1239, -4.0939]","-4.0669<br/>[-4.0806, -4.0527]","-4.0782<br/>[-4.0916, -4.0641]","-4.0399<br/>[-4.0528, -4.0265]","-4.0762<br/>[-4.0898, -4.0622]","-4.0320<br/>[-4.0448, -4.0188]","-4.0410<br/>[-4.0541, -4.0276]","-4.0330<br/>[-4.0455, -4.0200]","-4.0758<br/>[-4.0894, -4.0617]","-4.0315<br/>[-4.0443, -4.0183]","-4.0408<br/>[-4.0539, -4.0274]","-4.0313<br/>[-4.0440, -4.0180]","-4.0375<br/>[-4.0501, -4.0244]","-4.0363<br/>[-4.0492, -4.0231]","-4.0911<br/>[-4.1055, -4.0762]","-4.0360<br/>[-4.0489, -4.0227]","-4.0363<br/>[-4.0490, -4.0232]","-4.1004<br/>[-4.1129, -4.0877]","-4.0360<br/>[-4.0487, -4.0228]","-4.0409<br/>[-4.0540, -4.0275]","-4.0274<br/>[-4.0401, -4.0144]","-4.0745<br/>[-4.0882, -4.0603]","-4.0969<br/>[-4.1091, -4.0844]","-4.0698<br/>[-4.0816, -4.0579]","-4.0332<br/>[-4.0455, -4.0204]","-4.0738<br/>[-4.0874, -4.0596]","-4.0732<br/>[-4.0866, -4.0593]","-4.0300<br/>[-4.0427, -4.0168]","-4.0776<br/>[-4.0914, -4.0633]","-4.0776<br/>[-4.0914, -4.0633]","-4.0799<br/>[-4.0938, -4.0655]","-4.0799<br/>[-4.0938, -4.0655]","-4.0657<br/>[-4.0796, -4.0514]","-4.0878<br/>[-4.1017, -4.0733]","-4.0298<br/>[-4.0421, -4.0170]","-4.0668<br/>[-4.0804, -4.0527]","-4.0621<br/>[-4.0735, -4.0504]","-4.0686<br/>[-4.0825, -4.0543]","-4.0715<br/>[-4.0852, -4.0574]","-4.0583<br/>[-4.0717, -4.0445]","-4.0501<br/>[-4.0633, -4.0364]","-4.0488<br/>[-4.0620, -4.0352]","-4.0478<br/>[-4.0607, -4.0344]","-4.0385<br/>[-4.0511, -4.0254]","-4.0438<br/>[-4.0567, -4.0304]","-4.0293<br/>[-4.0418, -4.0163]","-4.0291<br/>[-4.0416, -4.0161]","-4.0347<br/>[-4.0473, -4.0215]","-4.0352<br/>[-4.0479, -4.0221]","-4.0315<br/>[-4.0442, -4.0184]","-4.0313<br/>[-4.0440, -4.0182]"],["-2.6270<br/>[-2.6270, -2.6270]","-2.4957<br/>[-2.4957, -2.4955]","-2.7861<br/>[-2.8034, -2.7706]","-2.7205<br/>[-2.7233, -2.7174]","-2.7379<br/>[-2.7408, -2.7348]","-2.3832<br/>[-2.3881, -2.3763]","-2.0218<br/>[-2.0925, -1.9856]","-2.1719<br/>[-2.2285, -2.1237]","-2.4580<br/>[-2.4806, -2.4350]","-2.5343<br/>[-2.6101, -2.4603]","-2.4904<br/>[-2.5238, -2.4571]","-2.0407<br/>[-2.0671, -2.0118]","-2.2301<br/>[-2.2315, -2.2253]","-1.5561<br/>[-1.5603, -1.5521]","-1.7678<br/>[-1.7782, -1.7556]","-1.8140<br/>[-1.8258, -1.7991]","-1.6233<br/>[-1.6507, -1.5736]","-1.8704<br/>[-1.8834, -1.8531]","-2.0225<br/>[-2.0351, -2.0053]","-2.1051<br/>[-2.1169, -2.0886]","-2.1361<br/>[-2.1474, -2.1205]","-2.1714<br/>[-2.1830, -2.1554]","-1.3426<br/>[-1.3893, -1.2226]","-2.2541<br/>[-2.2579, -2.2502]","-2.6841<br/>[-2.7554, -2.6290]","-2.6984<br/>[-2.7480, -2.6572]","-2.0519<br/>[-2.0609, -2.0411]","-1.9987<br/>[-2.0392, -1.9648]","-2.6104<br/>[-2.6203, -2.6060]","-2.1280<br/>[-2.1291, -2.1273]","-2.1344<br/>[-2.1350, -2.1340]","-2.1174<br/>[-2.1467, -2.0528]","-2.1174<br/>[-2.1467, -2.0528]","-2.1897<br/>[-2.2141, -2.1600]","-2.6935<br/>[-2.6961, -2.6870]","-2.3987<br/>[-2.4012, -2.3967]","-2.3987<br/>[-2.4012, -2.3967]","-1.6307<br/>[-1.6607, -1.5981]","-1.9402<br/>[-1.9666, -1.8544]","-1.6769<br/>[-1.6799, -1.6606]","-1.6483<br/>[-1.6631, -1.6290]","-2.6747<br/>[-2.6946, -2.6482]","-2.6877<br/>[-2.7062, -2.6612]","-2.5610<br/>[-2.5819, -2.5456]","-2.5654<br/>[-2.5839, -2.5488]","-2.5666<br/>[-2.5865, -2.5490]","-2.5698<br/>[-2.5895, -2.5518]","-2.2400<br/>[-2.2773, -2.2064]","-1.3143<br/>[-1.3484, -1.3021]","-2.6336<br/>[-2.6562, -2.6157]","-2.7353<br/>[-2.8207, -2.7120]","-2.3054<br/>[-2.3427, -2.2695]","-2.5487<br/>[-2.5543, -2.5354]","-2.3097<br/>[-2.3442, -2.2712]","-2.0520<br/>[-2.1518, -1.9866]","-2.1619<br/>[-2.2061, -2.1184]","-2.8295<br/>[-2.8645, -2.7936]","-2.4055<br/>[-2.4424, -2.3718]","-2.6822<br/>[-2.7330, -2.6296]","-2.3485<br/>[-2.3817, -2.3094]","-2.8461<br/>[-2.8866, -2.8041]","-2.6624<br/>[-2.6882, -2.6283]","-2.4807<br/>[-2.5195, -2.4437]","-2.7576<br/>[-2.7704, -2.7342]","-2.5109<br/>[-2.5456, -2.4700]","-2.7631<br/>[-2.7811, -2.7338]","-2.3922<br/>[-2.4021, -2.3782]","-2.8306<br/>[-2.8460, -2.8046]","-2.2011<br/>[-2.2464, -2.1560]","-2.3282<br/>[-2.3698, -2.2869]","-2.6576<br/>[-2.7037, -2.4995]","-2.0336<br/>[-2.0875, -1.9869]","-2.5520<br/>[-2.5985, -2.5293]","-3.2838<br/>[-3.3770, -3.1757]","-2.8391<br/>[-2.8460, -2.8115]","-3.0728<br/>[-3.0752, -3.0713]","-3.0820<br/>[-3.1113, -3.0397]","-2.8822<br/>[-2.9344, -2.6777]","-2.8822<br/>[-2.9344, -2.6777]","-3.0815<br/>[-3.0852, -3.0814]","-3.0815<br/>[-3.0852, -3.0814]","-2.8561<br/>[-2.8822, -2.8484]","-2.7075<br/>[-2.7161, -2.6903]","-3.2678<br/>[-3.2736, -3.2600]","-2.6057<br/>[-2.6257, -2.5871]","-1.4703<br/>[-1.4829, -1.4620]","-2.4673<br/>[-2.4710, -2.4331]","-2.3771<br/>[-2.3827, -2.3770]","-2.4768<br/>[-2.5017, -2.4660]","-2.9728<br/>[-3.0173, -2.9271]","-3.0781<br/>[-3.1325, -3.0298]","-3.4100<br/>[-3.5296, -3.2515]","-3.4792<br/>[-3.5560, -3.4099]","-3.4839<br/>[-3.6191, -3.3738]","-3.0646<br/>[-3.1553, -2.9910]","-3.0945<br/>[-3.1896, -3.0173]","-3.5451<br/>[-3.6493, -3.4596]","-3.0222<br/>[-3.1683, -2.9127]","-3.1479<br/>[-3.4265, -2.9865]","-3.2345<br/>[-3.4964, -3.0643]"]],"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":[["Adrenal Gland","Liver","Brain - Cerebellum","Brain - Cortex","Brain - Anterior cingulate cortex (BA24)","Brain - Frontal Cortex (BA9)","Brain - Hippocampus","Brain - Caudate (basal ganglia)","Brain - Nucleus accumbens (basal ganglia)","Brain - Hypothalamus","Brain - Putamen (basal ganglia)","Uterus","Prostate","Ovary","Cells - EBV-transformed lymphocytes","Pancreas","Pituitary","Skin - Not Sun Exposed (Suprapubic)","Skin - Sun Exposed (Lower leg)","Testis","Vagina","Breast - Mammary Tissue","Cells - Transformed fibroblasts","Small Intestine - Terminal Ileum","Esophagus - Muscularis","Spleen","Lung","Esophagus - Mucosa","Heart - Left Ventricle","Muscle - Skeletal","Artery - Coronary","Artery - Tibial","Artery - Aorta","Colon - Transverse","Stomach","Esophagus - Gastroesophageal Junction","Colon - Sigmoid","Brain - Cerebellar Hemisphere","Whole Blood","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Nerve - Tibial","Thyroid","Heart - Atrial Appendage"],[5361,6048,5395,5558,5640,5927,5487,6207,5839,5640,6273,5412,5325,5597,4742,4876,5617,5491,5430,5556,5508,5307,5845,4477,5725,3839,4780,5352,5344,5353,5895,5774,6066,4968,5012,5533,5630,5376,5604,5368,5565,5424,5886,5553],[52.0704554065734,49.3930228142375,48.0683537636795,45.5679449337702,45.3939236963975,44.9309613689794,44.168485122197,43.7259782596276,43.2078287470558,42.993083687603,42.5795668348474,15.4969548512149,15.2204093908507,11.8158171177728,11.4442912583134,11.323443013394,11.2320265923393,11.0557493903728,11.0038032467042,10.4323795904761,10.1476221544046,10.0567218825599,9.91884469654199,8.95632521403064,6.60875326483083,4.4674850728692,4.41952569143933,4.37213270295694,4.15600582602265,4.03453787007166,3.09980117937957,3.00844910018291,2.87977806443035,2.80757809943047,2.7869292483961,2.68070440795212,2.65259784404762,2.05387158601534,0.853367757813608,0.482281816026395,0.481431445708902,0.405456899455688,0.289076641127626,0.136154964136661],["-4.0732<br/>[-4.0872, -4.0588]","-4.0902<br/>[-4.1037, -4.0764]","-4.0687<br/>[-4.0821, -4.0547]","-4.0671<br/>[-4.0808, -4.0529]","-4.0671<br/>[-4.0808, -4.0529]","-4.0669<br/>[-4.0806, -4.0527]","-4.0629<br/>[-4.0766, -4.0488]","-4.0626<br/>[-4.0763, -4.0484]","-4.0627<br/>[-4.0765, -4.0485]","-4.0628<br/>[-4.0765, -4.0486]","-4.0625<br/>[-4.0763, -4.0484]","-4.0437<br/>[-4.0567, -4.0303]","-4.0435<br/>[-4.0565, -4.0301]","-4.0391<br/>[-4.0519, -4.0258]","-4.0391<br/>[-4.0519, -4.0257]","-4.0390<br/>[-4.0519, -4.0257]","-4.0389<br/>[-4.0517, -4.0256]","-4.0387<br/>[-4.0516, -4.0254]","-4.0388<br/>[-4.0516, -4.0255]","-4.0434<br/>[-4.0563, -4.0300]","-4.0352<br/>[-4.0480, -4.0219]","-4.0351<br/>[-4.0480, -4.0219]","-4.0349<br/>[-4.0477, -4.0217]","-4.0438<br/>[-4.0568, -4.0304]","-4.0300<br/>[-4.0428, -4.0168]","-4.0264<br/>[-4.0390, -4.0134]","-4.0262<br/>[-4.0388, -4.0132]","-4.0260<br/>[-4.0386, -4.0130]","-4.0258<br/>[-4.0384, -4.0128]","-4.0256<br/>[-4.0382, -4.0125]","-4.0303<br/>[-4.0430, -4.0171]","-4.0302<br/>[-4.0429, -4.0171]","-4.0301<br/>[-4.0428, -4.0170]","-4.0303<br/>[-4.0431, -4.0171]","-4.0303<br/>[-4.0430, -4.0171]","-4.0301<br/>[-4.0428, -4.0169]","-4.0300<br/>[-4.0428, -4.0169]","-4.0308<br/>[-4.0432, -4.0180]","-4.0265<br/>[-4.0389, -4.0136]","-4.0260<br/>[-4.0386, -4.0131]","-4.0260<br/>[-4.0385, -4.0130]","-4.0259<br/>[-4.0385, -4.0130]","-4.0257<br/>[-4.0383, -4.0127]","-4.0255<br/>[-4.0381, -4.0124]"],["-2.3941<br/>[-2.4299, -2.3595]","-2.3339<br/>[-2.3490, -2.3264]","-2.4511<br/>[-2.4853, -2.4179]","-2.5017<br/>[-2.5209, -2.4737]","-2.5068<br/>[-2.5261, -2.4827]","-2.5320<br/>[-2.5502, -2.5086]","-2.5059<br/>[-2.5280, -2.4777]","-2.5500<br/>[-2.5689, -2.5209]","-2.5479<br/>[-2.5619, -2.5299]","-2.5193<br/>[-2.5314, -2.4954]","-2.5730<br/>[-2.5859, -2.5481]","-2.7538<br/>[-2.8213, -2.6925]","-2.7600<br/>[-2.8312, -2.6952]","-2.8766<br/>[-2.9906, -2.7902]","-2.8919<br/>[-3.0037, -2.7959]","-2.9197<br/>[-3.0229, -2.8320]","-2.9401<br/>[-3.0217, -2.8645]","-2.9775<br/>[-3.0793, -2.8873]","-2.9574<br/>[-3.0297, -2.8808]","-2.5487<br/>[-2.5823, -2.5234]","-2.9874<br/>[-3.1285, -2.8709]","-2.9965<br/>[-3.0973, -2.9177]","-3.0307<br/>[-3.1792, -2.9167]","-2.7300<br/>[-2.7947, -2.6543]","-3.1340<br/>[-3.2387, -3.0269]","-3.3346<br/>[-3.5407, -3.1536]","-3.3554<br/>[-3.6227, -3.1674]","-3.4442<br/>[-3.6687, -3.2541]","-3.5568<br/>[-3.7007, -3.3965]","-3.6474<br/>[-3.7223, -3.5366]","-3.0422<br/>[-3.1920, -2.9266]","-3.0540<br/>[-3.1942, -2.9413]","-3.0898<br/>[-3.2210, -2.9802]","-3.0654<br/>[-3.1776, -2.9620]","-3.0721<br/>[-3.1812, -2.9698]","-3.1074<br/>[-3.2241, -2.9985]","-3.1163<br/>[-3.2348, -3.0092]","-3.1297<br/>[-3.2630, -3.0066]","-3.2403<br/>[-3.5601, -3.0732]","-3.3255<br/>[-3.7029, -3.1028]","-3.3258<br/>[-3.7174, -3.0948]","-3.3707<br/>[-3.7143, -3.1542]","-3.4558<br/>[-3.7538, -3.2527]","-3.5379<br/>[-3.7558, -3.3576]"]],"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":[["Testis","Liver","Kidney_Cortex","Adrenal_Gland","Breast_Mammary_Tissue","Adipose_Subcutaneous","Small_Intestine_Terminal_Ileum","Adipose_Visceral_(Omentum)","Uterus","Stomach","Brain_Cortex","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Frontal_Cortex_(BA9)","Prostate","Minor_Salivary_Gland","Brain_Hippocampus","Brain_Amygdala","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Hypothalamus","Brain_Substantia_nigra","Artery_Tibial","Artery_Aorta","Esophagus_Gastroesophageal_Junction","Heart_Atrial_Appendage","Heart_Left_Ventricle","Colon_Sigmoid","Artery_Coronary","Esophagus_Muscularis","Colon_Transverse","Esophagus_Mucosa","Thyroid","Vagina","Nerve_Tibial","Brain_Cerebellum","Cells_Transformed_fibroblasts","Brain_Cerebellar_Hemisphere","Whole_Blood","Spleen","Ovary","Cells_EBV-transformed_lymphocytes","Pancreas","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Muscle_Skeletal","Lung","Pituitary","Brain_Spinal_cord_(cervical_c-1)"],[7350,7802,8549,11764,9405,9708,8318,9405,12030,8858,11476,11221,11293,10900,13167,8710,8003,10489,10756,12484,11718,12225,12095,13755,13582,10637,10542,10522,11905,13752,7141,6519,11536,6415,11965,10458,10342,13068,6787,6835,11108,7446,7325,6475,6558,8257,7960,9113,12198],[831.624249328303,78.3018068012931,47.33184794992,38.5302348195227,8.76710498352084,7.10365218679871,7.00076792924858,4.46206092714211,3.47606082078827,3.45912546581733,2.47374851612024,2.43508707805053,2.41127313691331,2.41041679833768,2.28939426529292,1.91219123422169,1.81919700188814,1.69378070105506,1.65833163349494,1.5875085727687,1.55844908526278,1.5172162375537,0.686210709514993,0.633230195471363,0.613431569452819,0.592498805066991,0.556161305763991,0.432985339464681,0.364528212952307,0.313794039513618,0.175882809410624,0.0849480160320504,-0.0102210704555253,-0.0150314809925611,-0.166370834736919,-0.237266598615805,-0.312335353563115,-0.409497108081871,-0.529549788358677,-0.531151135749514,-0.578908327331269,-0.58102441372352,-0.653375816287891,-0.656502647582483,-0.659668300290412,-0.759506349467074,-0.760032638351012,-0.781047302410597,-0.840224235878113],["-4.0292<br/>[-4.0419, -4.0160]","-4.1244<br/>[-4.1383, -4.1102]","-4.0613<br/>[-4.0748, -4.0474]","-4.0603<br/>[-4.0740, -4.0462]","-4.0383<br/>[-4.0512, -4.0250]","-4.0312<br/>[-4.0436, -4.0184]","-4.0424<br/>[-4.0553, -4.0290]","-4.0380<br/>[-4.0499, -4.0258]","-4.0387<br/>[-4.0515, -4.0255]","-4.0371<br/>[-4.0498, -4.0239]","-4.0319<br/>[-4.0447, -4.0186]","-4.0320<br/>[-4.0448, -4.0187]","-4.0319<br/>[-4.0447, -4.0187]","-4.0320<br/>[-4.0449, -4.0188]","-4.0312<br/>[-4.0440, -4.0179]","-4.0330<br/>[-4.0459, -4.0198]","-4.0327<br/>[-4.0453, -4.0195]","-4.0323<br/>[-4.0451, -4.0190]","-4.0322<br/>[-4.0450, -4.0189]","-4.0315<br/>[-4.0443, -4.0182]","-4.0317<br/>[-4.0445, -4.0185]","-4.0315<br/>[-4.0443, -4.0182]","-4.0273<br/>[-4.0400, -4.0141]","-4.0265<br/>[-4.0393, -4.0134]","-4.0268<br/>[-4.0395, -4.0137]","-4.0324<br/>[-4.0453, -4.0191]","-4.0234<br/>[-4.0360, -4.0103]","-4.0278<br/>[-4.0406, -4.0147]","-4.0273<br/>[-4.0401, -4.0141]","-4.0267<br/>[-4.0395, -4.0136]","-4.0289<br/>[-4.0415, -4.0159]","-4.0256<br/>[-4.0381, -4.0126]","-4.0277<br/>[-4.0404, -4.0145]","-4.0254<br/>[-4.0380, -4.0124]","-4.0228<br/>[-4.0354, -4.0097]","-4.0259<br/>[-4.0381, -4.0133]","-4.0278<br/>[-4.0405, -4.0146]","-4.0248<br/>[-4.0370, -4.0122]","-4.0257<br/>[-4.0382, -4.0128]","-4.0257<br/>[-4.0382, -4.0128]","-4.0231<br/>[-4.0358, -4.0101]","-4.0254<br/>[-4.0379, -4.0124]","-4.0251<br/>[-4.0376, -4.0121]","-4.0252<br/>[-4.0378, -4.0122]","-4.0252<br/>[-4.0378, -4.0122]","-4.0243<br/>[-4.0369, -4.0113]","-4.0244<br/>[-4.0370, -4.0113]","-4.0239<br/>[-4.0366, -4.0109]","-4.0227<br/>[-4.0353, -4.0096]"],["-3.2629<br/>[-3.2635, -3.2618]","-2.1730<br/>[-2.1733, -2.1728]","-2.6778<br/>[-2.6973, -2.6451]","-2.9090<br/>[-2.9453, -2.7858]","-3.2648<br/>[-3.2761, -3.2443]","-3.0056<br/>[-3.0826, -2.9365]","-2.9796<br/>[-3.0592, -2.9091]","-3.1407<br/>[-3.1897, -3.0676]","-3.3275<br/>[-3.3776, -3.2751]","-3.2783<br/>[-3.3976, -3.1828]","-3.5058<br/>[-3.5972, -3.4259]","-3.5131<br/>[-3.5917, -3.4378]","-3.5213<br/>[-3.5962, -3.4492]","-3.5195<br/>[-3.5823, -3.4559]","-3.5728<br/>[-3.6600, -3.4935]","-3.5334<br/>[-3.6265, -3.4369]","-3.5497<br/>[-3.6167, -3.4787]","-3.6431<br/>[-3.7114, -3.5657]","-3.6602<br/>[-3.7229, -3.5851]","-3.7037<br/>[-3.7826, -3.6174]","-3.7118<br/>[-3.7627, -3.6474]","-3.7345<br/>[-3.7808, -3.6735]","-3.6144<br/>[-3.7393, -3.5260]","-3.6452<br/>[-3.7842, -3.5388]","-3.6531<br/>[-3.7861, -3.5546]","-3.6193<br/>[-3.7056, -3.5285]","-3.8801<br/>[-4.0090, -3.7205]","-3.6857<br/>[-3.7178, -3.6404]","-3.7244<br/>[-3.7689, -3.6644]","-3.7626<br/>[-3.8226, -3.6886]","-3.5520<br/>[-3.8423, -3.3650]","-3.5856<br/>[-3.8533, -3.4003]","-3.7485<br/>[-3.9833, -3.5633]","-3.6599<br/>[-3.8690, -3.5090]","-3.8584<br/>[-4.0424, -3.7167]","-3.8031<br/>[-4.2359, -3.5959]","-3.9686<br/>[-4.0284, -3.8919]","-3.9720<br/>[-4.3730, -3.7663]","-4.0609<br/>[-4.6237, -3.7500]","-4.0665<br/>[-4.6114, -3.7618]","-4.1698<br/>[-4.5117, -3.9498]","-4.1704<br/>[-4.6838, -3.8654]","-4.3601<br/>[-4.9472, -3.9406]","-4.4653<br/>[-5.0402, -4.0784]","-4.4741<br/>[-5.0338, -4.0873]","-5.0646<br/>[-5.7795, -4.6252]","-5.2371<br/>[-5.9826, -4.7814]","-5.1312<br/>[-5.7859, -4.6972]","-5.1708<br/>[-5.7800, -4.7541]"]],"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":[["20","19","18","16","4","9","2","1","3","13","7","10","11","6","5","14","17","8","12","15"],[7643,5554,6884,9734,11777,9065,8428,7017,9555,7158,7753,7847,9849,8324,10930,8926,7959,9695,6819,7282],[55.970799696169,27.3087120739373,7.88511859738518,6.26711909026508,5.06908520013794,3.05299825116557,2.85681693600718,2.30723977369433,2.08889751871904,1.38297087010023,1.2946823994595,0.979125154029098,0.87361947479212,0.743196150846694,0.703216350441884,-0.0725796340809404,-0.446874773299393,-0.571003711405703,-0.606908675667966,-0.620297551273622],["-4.0948<br/>[-4.1085, -4.0809]","-4.0337<br/>[-4.0463, -4.0205]","-4.0380<br/>[-4.0509, -4.0247]","-4.0482<br/>[-4.0610, -4.0349]","-4.0472<br/>[-4.0603, -4.0337]","-4.0377<br/>[-4.0507, -4.0242]","-4.0342<br/>[-4.0466, -4.0213]","-4.0308<br/>[-4.0433, -4.0179]","-4.0351<br/>[-4.0477, -4.0222]","-4.0340<br/>[-4.0469, -4.0207]","-4.0245<br/>[-4.0372, -4.0115]","-4.0334<br/>[-4.0462, -4.0201]","-4.0284<br/>[-4.0411, -4.0153]","-4.0289<br/>[-4.0416, -4.0157]","-4.0281<br/>[-4.0408, -4.0149]","-4.0284<br/>[-4.0411, -4.0153]","-4.0253<br/>[-4.0378, -4.0124]","-4.0246<br/>[-4.0371, -4.0118]","-4.0250<br/>[-4.0377, -4.0120]","-4.0251<br/>[-4.0377, -4.0121]"],["-2.3841<br/>[-2.3978, -2.3757]","-2.9095<br/>[-2.9242, -2.8848]","-3.0074<br/>[-3.0289, -2.9716]","-3.0385<br/>[-3.1179, -2.9721]","-3.2008<br/>[-3.2643, -3.1419]","-3.2865<br/>[-3.3405, -3.2287]","-3.3060<br/>[-3.4646, -3.1791]","-3.1110<br/>[-3.2692, -2.9924]","-3.3306<br/>[-3.4399, -3.2453]","-3.3116<br/>[-3.4884, -3.1811]","-3.3975<br/>[-3.4455, -3.3599]","-3.4552<br/>[-3.5753, -3.3509]","-3.5068<br/>[-3.6736, -3.3860]","-3.5121<br/>[-3.6481, -3.3986]","-3.5885<br/>[-3.7127, -3.4789]","-3.7910<br/>[-3.9294, -3.6306]","-3.9721<br/>[-4.5890, -3.6324]","-4.2156<br/>[-4.6942, -3.9181]","-4.3832<br/>[-5.0583, -3.9503]","-4.4467<br/>[-4.9502, -4.0868]"]],"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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