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<h1 class="title toc-ignore">Enrichment results of packed cell volume</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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<p><summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/xiangzhu/rss-gsea/tree/1ac8c289a58f3030d8a28c3b85ac1e3ee9292fe8" target="_blank">1ac8c28</a> </summary></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/23222517">“Seventy-Five Genetic Loci Influencing the Human Red Blood Cell” (<em>Nature</em>, 2012)</a>. The summary data file is available from the European Genome–Phenome Archive (EGA, <a href="http://www.ebi.ac.uk/ega" class="uri">http://www.ebi.ac.uk/ega</a>) under accession number EGAS00000000132.</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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glutamate receptors<br/>(biocarta, BioCarta)","RNF mutants show enhanced WNT signaling and proliferation<br/>(reactome, BioSystems)","glutamate dependent acid resistance<br/>(humancyc, PC)","Adrenaline and noradrenaline biosynthesis<br/>(panther, PC)","Sema4D in semaphorin signaling<br/>(reactome, PC)","Notch signaling pathway<br/>(panther, PANTHER)","Tyrosine metabolism<br/>(kegg, BioSystems)","Striated Muscle Contraction<br/>(reactome, BioSystems)","NOTCH1 Intracellular Domain Regulates Transcription<br/>(reactome, PC)","Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants<br/>(reactome, PC)","Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants<br/>(reactome, BioSystems)","Valine, leucine and...<br/>(kegg, PC)","FBXW7 Mutants and NOTCH1 in Cancer<br/>(reactome, PC)","Signaling by NOTCH1<br/>(reactome, BioSystems)","Nicotine Activity on Dopaminergic Neurons<br/>(wiki, BioSystems)","Delta-Notch Signaling Pathway<br/>(wiki, BioSystems)","Validated targets of C-MYC transcriptional repression<br/>(pid, PC)","Synthesis of PIPs at the late endosome membrane<br/>(reactome, PC)","Synthesis of PIPs at the early endosome membrane<br/>(reactome, PC)","COPI Mediated Transport<br/>(reactome, PC)","Muscle contraction<br/>(reactome, BioSystems)","COPI Mediated Transport<br/>(reactome, BioSystems)","Heme biosynthesis<br/>(panther, PC)","Semaphorin interactions<br/>(reactome, PC)","regulation of FZD by ubiquitination<br/>(reactome, PC)","Signaling by NOTCH<br/>(reactome, PC)","Signaling by WNT in cancer<br/>(reactome, BioSystems)","Serotonin receptors<br/>(reactome, PC)","Signaling by NOTCH<br/>(reactome, BioSystems)","Downregulation of TGF-beta receptor signaling<br/>(reactome, PC)","TGF-beta receptor signaling activates SMADs<br/>(reactome, PC)"],[2,59,27,25,41,24,26,53,51,22,111,62,103,68,99,100,103,60,101,105,37,75,85,83,91,10,72,86,75,88,103,35,44,18,36,45,46,46,63,37,37,48,99,32,8,38,13,8,5,3,46,9,4,5,39,42,15,5,15,30,37,13,16,13,11,18,7,3,17,8,3,23,27,37,33,33,43,52,53,5,67,68,21,83,63,9,12,10,64,11,10,64,21,105,32,11,106,26,32],[257,1125,3150,2869,3948,2300,3052,5630,5471,2414,5514,1869,4402,1998,4470,4566,4471,2600,4288,4360,3319,3850,2962,3091,3084,938,3824,3617,3312,3994,4246,2923,4452,2071,6026,4540,4595,4628,6239,3564,6125,4871,11893,3872,741,4267,1836,658,375,387,5110,871,471,553,3588,3834,3139,845,1641,2722,3400,1377,1376,1554,1021,1390,933,469,2119,768,347,2479,2493,3171,2906,2898,5169,5674,5815,406,7560,7701,2237,8031,6134,1006,1434,669,6284,785,962,8315,2245,10667,3285,1163,10808,2517,3067],[664.088197241327,217.460572468456,160.658915068929,159.927729188904,20.0363272266565,18.357655444347,15.14087948377,4.89464968634371,3.35500028409359,3.03505973251936,1.86785112985736,1.74383284659623,1.54665280595808,1.53918804966127,1.52840656407729,1.47660404983178,1.46105319607311,1.43274749698819,1.38253382219378,1.37389848380095,1.36980127669775,1.36448197849184,1.31894200332922,1.31376946308103,1.31037114706656,1.28680855903516,1.26938106195235,1.22602567805723,1.20544186290503,1.18464202976468,1.18174225774839,1.16498901743729,1.086826446619,1.0653467598503,0.920470359983375,0.908038114924074,0.905257579454283,0.898535319810969,0.883579353850657,0.870402028899337,0.868085108635044,0.861268074041068,0.595684840538783,0.349328828790319,0.344662893871395,0.31805879162121,0.0754426505777919,0.0752684318380069,0.069483244965339,0.0619752267498897,0.0568985259647205,0.0539601377481236,0.0454494228138308,0.0340699660904954,0.0142982593483398,0.011631509537315,0.00886491919288408,0.00176364859316896,-0.0196812309147916,-0.0200098048569437,-0.0261236330267879,-0.0302005714289362,-0.0325109975268321,-0.0356955035660042,-0.0393599982485958,-0.0395327618251583,-0.0401180307228988,-0.0436880253292215,-0.045584621501436,-0.055858452150464,-0.056601761118024,-0.0747055958781726,-0.0789338787615148,-0.0915686466563081,-0.097148390780667,-0.111307525730779,-0.124335125018541,-0.132591592522146,-0.134194833271445,-0.143087733830708,-0.154628744867528,-0.155954341335702,-0.158571605537795,-0.164681223581477,-0.183588127940598,-0.186890077749762,-0.221197447583675,-0.221498123745242,-0.230458532540353,-0.237743306282258,-0.243853145294571,-0.252104101435921,-0.255991830605759,-0.266976615383483,-0.284281819458942,-0.288392737533659,-0.292864834445176,-0.329668712593327,-0.337947934544739],["-4.8803<br/>[-4.8804, -4.8766]","-4.9121<br/>[-4.9122, -4.9084]","-4.8854<br/>[-4.8855, -4.8821]","-4.8855<br/>[-4.8856, -4.8822]","-4.8790<br/>[-4.8791, -4.8752]","-4.8795<br/>[-4.8796, -4.8758]","-4.8794<br/>[-4.8795, -4.8757]","-4.9420<br/>[-4.9421, -4.9377]","-4.9421<br/>[-4.9422, -4.9378]","-4.8795<br/>[-4.8796, -4.8758]","-4.9105<br/>[-4.9106, -4.9069]","-4.9118<br/>[-4.9119, -4.9082]","-4.9113<br/>[-4.9114, -4.9077]","-4.9118<br/>[-4.9119, -4.9081]","-4.9109<br/>[-4.9110, -4.9073]","-4.9109<br/>[-4.9110, -4.9072]","-4.9113<br/>[-4.9114, -4.9077]","-4.9115<br/>[-4.9117, -4.9079]","-4.9114<br/>[-4.9115, -4.9077]","-4.9109<br/>[-4.9110, -4.9072]","-4.9099<br/>[-4.9101, -4.9060]","-4.9115<br/>[-4.9116, -4.9079]","-4.9114<br/>[-4.9115, -4.9078]","-4.9114<br/>[-4.9115, -4.9077]","-4.9114<br/>[-4.9115, -4.9077]","-4.9105<br/>[-4.9106, -4.9065]","-4.9123<br/>[-4.9124, -4.9087]","-4.9112<br/>[-4.9113, -4.9075]","-4.9113<br/>[-4.9114, -4.9076]","-4.9110<br/>[-4.9111, -4.9073]","-4.9109<br/>[-4.9110, -4.9073]","-4.8794<br/>[-4.8795, -4.8756]","-4.8926<br/>[-4.8927, -4.8894]","-4.8796<br/>[-4.8797, -4.8759]","-4.9087<br/>[-4.9088, -4.9047]","-4.9091<br/>[-4.9092, -4.9051]","-4.9091<br/>[-4.9092, -4.9051]","-4.8787<br/>[-4.8788, -4.8750]","-4.8920<br/>[-4.8921, -4.8888]","-4.8930<br/>[-4.8931, -4.8898]","-4.9087<br/>[-4.9088, -4.9047]","-4.8786<br/>[-4.8787, -4.8749]","-4.9065<br/>[-4.9066, -4.9025]","-4.8808<br/>[-4.8809, -4.8771]","-4.8835<br/>[-4.8836, -4.8798]","-4.8806<br/>[-4.8807, -4.8770]","-4.8803<br/>[-4.8804, -4.8766]","-4.8801<br/>[-4.8803, -4.8764]","-4.8804<br/>[-4.8805, -4.8767]","-4.8803<br/>[-4.8804, -4.8765]","-4.8819<br/>[-4.8820, -4.8782]","-4.8801<br/>[-4.8802, -4.8763]","-4.8802<br/>[-4.8803, -4.8765]","-4.8802<br/>[-4.8803, -4.8765]","-4.8826<br/>[-4.8827, -4.8789]","-4.8825<br/>[-4.8826, -4.8788]","-4.8798<br/>[-4.8799, -4.8761]","-4.8800<br/>[-4.8801, -4.8763]","-4.8798<br/>[-4.8799, -4.8761]","-4.8795<br/>[-4.8796, -4.8758]","-4.8793<br/>[-4.8794, -4.8756]","-4.8799<br/>[-4.8800, -4.8762]","-4.8797<br/>[-4.8798, -4.8760]","-4.8798<br/>[-4.8799, -4.8760]","-4.8798<br/>[-4.8799, -4.8761]","-4.8797<br/>[-4.8798, -4.8760]","-4.8799<br/>[-4.8800, -4.8761]","-4.8800<br/>[-4.8801, -4.8763]","-4.8797<br/>[-4.8798, -4.8760]","-4.8799<br/>[-4.8800, -4.8762]","-4.8801<br/>[-4.8802, -4.8763]","-4.8795<br/>[-4.8796, -4.8757]","-4.8794<br/>[-4.8795, -4.8757]","-4.8790<br/>[-4.8791, -4.8753]","-4.8793<br/>[-4.8794, -4.8756]","-4.8795<br/>[-4.8796, -4.8758]","-4.8783<br/>[-4.8784, -4.8745]","-4.8781<br/>[-4.8782, -4.8744]","-4.8781<br/>[-4.8782, -4.8743]","-4.8801<br/>[-4.8802, -4.8763]","-4.8774<br/>[-4.8775, -4.8737]","-4.8773<br/>[-4.8774, -4.8736]","-4.8797<br/>[-4.8798, -4.8760]","-4.8772<br/>[-4.8773, -4.8734]","-4.8780<br/>[-4.8782, -4.8743]","-4.8798<br/>[-4.8799, -4.8761]","-4.8797<br/>[-4.8798, -4.8759]","-4.8800<br/>[-4.8801, -4.8762]","-4.8782<br/>[-4.8783, -4.8745]","-4.8799<br/>[-4.8800, -4.8762]","-4.8798<br/>[-4.8799, -4.8761]","-4.8772<br/>[-4.8773, -4.8735]","-4.8794<br/>[-4.8795, -4.8757]","-4.8762<br/>[-4.8763, -4.8725]","-4.8791<br/>[-4.8792, -4.8754]","-4.8798<br/>[-4.8799, -4.8760]","-4.8761<br/>[-4.8762, -4.8724]","-4.8793<br/>[-4.8794, -4.8755]","-4.8791<br/>[-4.8792, -4.8753]"],["-1.2501<br/>[-1.2501, -1.2498]","-2.0506<br/>[-2.0566, -2.0403]","-2.5042<br/>[-2.8486, -2.4351]","-2.7972<br/>[-2.8386, -2.7560]","-2.8110<br/>[-2.8773, -2.7501]","-2.7217<br/>[-2.7543, -2.6827]","-2.9534<br/>[-3.0057, -2.8989]","-3.0742<br/>[-3.2230, -2.9568]","-3.2176<br/>[-3.2431, -3.2043]","-2.6953<br/>[-2.7899, -2.6951]","-3.3881<br/>[-3.4701, -3.3115]","-2.9821<br/>[-3.0338, -2.9608]","-3.3116<br/>[-3.4117, -3.2689]","-3.0236<br/>[-3.0846, -2.9986]","-3.3539<br/>[-3.4285, -3.3214]","-3.3675<br/>[-3.4450, -3.3347]","-3.3287<br/>[-3.4307, -3.2856]","-3.1436<br/>[-3.2128, -3.1158]","-3.3221<br/>[-3.4257, -3.2765]","-3.3635<br/>[-3.4430, -3.3320]","-3.2447<br/>[-3.5110, -3.0480]","-3.2809<br/>[-3.3840, -3.2392]","-3.2054<br/>[-3.2878, -3.1749]","-3.2249<br/>[-3.3066, -3.1946]","-3.2255<br/>[-3.3060, -3.1960]","-2.9546<br/>[-2.9715, -2.9382]","-3.2769<br/>[-3.3887, -3.2261]","-3.2970<br/>[-3.3906, -3.2642]","-3.2630<br/>[-3.3529, -3.2292]","-3.3462<br/>[-3.4390, -3.3123]","-3.3709<br/>[-3.4650, -3.3358]","-3.2635<br/>[-3.5016, -3.0684]","-3.3913<br/>[-3.4956, -3.3309]","-3.2248<br/>[-3.3459, -3.1465]","-3.6719<br/>[-3.7741, -3.5361]","-3.6390<br/>[-3.6563, -3.6170]","-3.6441<br/>[-3.6615, -3.6218]","-3.4841<br/>[-3.7753, -3.2755]","-3.4195<br/>[-3.7563, -3.2150]","-3.4200<br/>[-3.6521, -3.2276]","-3.6719<br/>[-3.7825, -3.5227]","-3.5132<br/>[-3.8196, -3.3129]","-3.9765<br/>[-4.0692, -3.8373]","-3.4324<br/>[-4.6523, -3.1574]","-3.0652<br/>[-3.8220, -2.9002]","-3.4316<br/>[-4.7433, -3.1244]","-3.7404<br/>[-4.7849, -3.3208]","-3.3881<br/>[-4.5861, -2.9436]","-3.1882<br/>[-4.3885, -2.7230]","-3.2108<br/>[-4.5986, -2.7378]","-4.2620<br/>[-4.7289, -3.9793]","-3.5213<br/>[-4.7049, -3.0589]","-3.3481<br/>[-4.6830, -2.8597]","-3.4200<br/>[-4.7517, -2.9166]","-4.4852<br/>[-4.9022, -4.2133]","-4.4990<br/>[-4.9303, -4.2283]","-3.8866<br/>[-5.0092, -3.3990]","-3.7627<br/>[-5.0150, -3.2363]","-4.2319<br/>[-5.1971, -3.7119]","-4.3987<br/>[-5.2166, -3.9678]","-4.5604<br/>[-5.3085, -4.1455]","-3.9828<br/>[-5.1299, -3.4228]","-4.7668<br/>[-5.7816, -4.2680]","-4.1424<br/>[-5.2705, -3.5874]","-5.3003<br/>[-6.5264, -4.7164]","-4.7207<br/>[-5.7853, -4.2091]","-5.2444<br/>[-6.5136, -4.6446]","-4.4352<br/>[-6.0307, -3.7899]","-4.3197<br/>[-5.1302, -3.8173]","-4.8247<br/>[-6.3044, -4.1777]","-4.6367<br/>[-6.4316, -3.9479]","-4.3466<br/>[-5.3717, -3.7838]","-4.3709<br/>[-5.4547, -3.8003]","-5.1994<br/>[-6.2875, -4.6191]","-4.4464<br/>[-5.4444, -3.8730]","-4.2004<br/>[-5.2432, -3.6465]","-5.2560<br/>[-6.2329, -4.6953]","-5.2245<br/>[-6.1941, -4.6482]","-5.1972<br/>[-6.1653, -4.6378]","-4.4061<br/>[-6.3147, -3.7185]","-5.3476<br/>[-6.2566, -4.7962]","-5.3227<br/>[-6.2303, -4.7690]","-4.2071<br/>[-5.1471, -3.6323]","-5.4576<br/>[-6.3699, -4.8863]","-4.8344<br/>[-5.7684, -4.2652]","-4.6241<br/>[-6.2267, -3.9680]","-4.8126<br/>[-6.3059, -4.1676]","-4.7003<br/>[-6.4687, -4.0279]","-4.7028<br/>[-5.5562, -4.1879]","-4.7850<br/>[-6.4980, -4.1147]","-4.8663<br/>[-6.5108, -4.2046]","-5.0532<br/>[-5.9037, -4.5268]","-4.6924<br/>[-5.9440, -4.0977]","-5.4465<br/>[-6.3186, -4.9019]","-4.6013<br/>[-5.7553, -4.0216]","-5.0877<br/>[-6.6673, -4.4337]","-5.4245<br/>[-6.2960, -4.8790]","-4.8296<br/>[-6.1523, -4.2115]","-4.9381<br/>[-6.1990, -4.3299]"]],"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","Brain - Hypothalamus","Brain - Cerebellar Hemisphere","Brain - Nucleus accumbens (basal ganglia)","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)","Heart - Left Ventricle","Brain - Cerebellum","Prostate","Brain - Cortex","Esophagus - Gastroesophageal Junction","Colon - Sigmoid","Artery - Aorta","Artery - Coronary","Adipose - Visceral (Omentum)","Brain - Anterior cingulate cortex (BA24)","Thyroid","Spleen","Small Intestine - Terminal Ileum","Lung","Nerve - Tibial","Testis","Brain - Hippocampus","Esophagus - Mucosa","Whole Blood","Esophagus - Muscularis","Artery - Tibial","Colon - Transverse","Stomach","Adipose - Subcutaneous","Pancreas","Pituitary","Skin - Not Sun Exposed (Suprapubic)","Ovary","Uterus","Cells - EBV-transformed lymphocytes","Cells - Transformed fibroblasts","Breast - Mammary Tissue","Vagina","Skin - Sun Exposed (Lower leg)","Adrenal Gland","Brain - Frontal Cortex (BA9)","Liver"],[6206,6007,6247,6010,6494,6903,6980,5948,6062,5952,6222,6147,6254,6728,6564,6227,6296,6545,4290,4987,5336,6055,6266,6107,5949,6244,6353,6424,5543,5591,5995,5454,6251,6168,6237,6030,5272,6475,5944,6153,6090,6006,6588,6701],[945.378757792677,869.984697907576,775.639226197909,738.487756803297,674.954558968863,674.828335521524,674.766483863578,584.841963071862,544.792588950689,477.433088535096,434.578519067267,434.554510138381,434.531477025573,434.503975311558,433.457341963876,366.801947813027,366.789053877002,366.709022887557,338.160126165902,337.973091790743,337.918983239228,337.767818131596,337.755959376011,337.750662331388,337.7362555377,337.732829841113,337.708265055902,337.680716223842,337.361704295214,337.361550694123,336.940345967032,281.13199229721,272.326337550421,271.983701970378,271.666916025899,271.508584533957,270.761394549603,269.718217982682,268.577411278826,267.347921053846,267.239770776515,243.639469492523,-0.50289246937115,-0.506942319504031],["-4.8789<br/>[-4.8790, -4.8753]","-4.8794<br/>[-4.8795, -4.8758]","-4.8782<br/>[-4.8783, -4.8745]","-4.8788<br/>[-4.8789, -4.8751]","-4.8785<br/>[-4.8786, -4.8748]","-4.8783<br/>[-4.8784, -4.8746]","-4.8783<br/>[-4.8784, -4.8746]","-4.8790<br/>[-4.8791, -4.8754]","-4.8788<br/>[-4.8789, -4.8751]","-5.0162<br/>[-5.0164, -5.0111]","-4.8787<br/>[-4.8788, -4.8750]","-4.8784<br/>[-4.8785, -4.8747]","-4.8784<br/>[-4.8785, -4.8747]","-4.8779<br/>[-4.8780, -4.8742]","-4.8779<br/>[-4.8781, -4.8742]","-4.8781<br/>[-4.8782, -4.8744]","-4.8782<br/>[-4.8783, -4.8745]","-4.8780<br/>[-4.8781, -4.8742]","-4.8790<br/>[-4.8791, -4.8753]","-4.8786<br/>[-4.8787, -4.8749]","-4.8784<br/>[-4.8785, -4.8747]","-4.8781<br/>[-4.8782, -4.8744]","-4.8788<br/>[-4.8789, -4.8751]","-4.8783<br/>[-4.8784, -4.8746]","-4.8782<br/>[-4.8783, -4.8745]","-4.8782<br/>[-4.8783, -4.8745]","-4.8783<br/>[-4.8784, -4.8746]","-4.8780<br/>[-4.8781, -4.8743]","-4.8788<br/>[-4.8789, -4.8751]","-4.8783<br/>[-4.8784, -4.8746]","-4.8782<br/>[-4.8783, -4.8745]","-5.0166<br/>[-5.0168, -5.0115]","-5.0163<br/>[-5.0165, -5.0112]","-5.0162<br/>[-5.0164, -5.0111]","-5.0161<br/>[-5.0163, -5.0110]","-5.0162<br/>[-5.0163, -5.0111]","-5.0165<br/>[-5.0166, -5.0114]","-5.0160<br/>[-5.0162, -5.0109]","-5.0162<br/>[-5.0164, -5.0111]","-5.0161<br/>[-5.0163, -5.0110]","-5.0162<br/>[-5.0164, -5.0111]","-5.0170<br/>[-5.0172, -5.0120]","-4.8779<br/>[-4.8780, -4.8741]","-4.8777<br/>[-4.8778, -4.8739]"],["-2.7592<br/>[-2.7593, -2.7583]","-2.7354<br/>[-2.7357, -2.7345]","-2.9093<br/>[-2.9110, -2.9093]","-2.8181<br/>[-2.8205, -2.8178]","-2.9627<br/>[-2.9653, -2.9599]","-2.9864<br/>[-2.9904, -2.9824]","-2.9940<br/>[-2.9968, -2.9913]","-2.7896<br/>[-2.8079, -2.7724]","-3.1941<br/>[-3.1957, -3.1870]","-2.6863<br/>[-2.6863, -2.6852]","-3.3061<br/>[-3.3133, -3.2974]","-3.3060<br/>[-3.3098, -3.3013]","-3.3137<br/>[-3.3173, -3.3092]","-3.3345<br/>[-3.3504, -3.2220]","-3.3396<br/>[-3.3396, -3.3396]","-3.3158<br/>[-3.3168, -3.3142]","-3.3166<br/>[-3.3206, -3.3121]","-3.3376<br/>[-3.3385, -3.3363]","-3.1483<br/>[-3.1540, -3.1426]","-3.2187<br/>[-3.2204, -3.2165]","-3.2486<br/>[-3.2498, -3.2470]","-3.3036<br/>[-3.3047, -3.3022]","-3.3058<br/>[-3.3156, -3.2933]","-3.3028<br/>[-3.3072, -3.2976]","-3.2961<br/>[-3.2971, -3.2949]","-3.3127<br/>[-3.3170, -3.3079]","-3.3186<br/>[-3.3240, -3.3122]","-3.3293<br/>[-3.3304, -3.3278]","-3.2493<br/>[-3.2537, -3.2403]","-3.2679<br/>[-3.2687, -3.2666]","-3.2974<br/>[-3.2981, -3.2959]","-2.6536<br/>[-2.6537, -2.6523]","-2.7131<br/>[-2.7148, -2.7118]","-2.7193<br/>[-2.7194, -2.7180]","-2.7336<br/>[-2.7353, -2.7323]","-2.7240<br/>[-2.7240, -2.7226]","-2.6730<br/>[-2.6744, -2.6719]","-2.7506<br/>[-2.7523, -2.7493]","-2.7218<br/>[-2.7219, -2.7207]","-2.7336<br/>[-2.7337, -2.7324]","-2.7174<br/>[-2.7175, -2.7162]","-2.7449<br/>[-2.7451, -2.7434]","-4.9529<br/>[-5.8382, -4.4364]","-5.0088<br/>[-5.8359, -4.5004]"]],"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":[["Cells_EBV-transformed_lymphocytes","Brain_Hypothalamus","Artery_Aorta","Brain_Cerebellum","Brain_Frontal_Cortex_(BA9)","Brain_Cerebellar_Hemisphere","Brain_Hippocampus","Brain_Amygdala","Breast_Mammary_Tissue","Nerve_Tibial","Kidney_Cortex","Minor_Salivary_Gland","Brain_Cortex","Brain_Anterior_cingulate_cortex_(BA24)","Artery_Tibial","Heart_Atrial_Appendage","Heart_Left_Ventricle","Prostate","Liver","Colon_Sigmoid","Cells_Transformed_fibroblasts","Whole_Blood","Skin_Sun_Exposed_(Lower_leg)","Vagina","Skin_Not_Sun_Exposed_(Suprapubic)","Esophagus_Mucosa","Pancreas","Spleen","Colon_Transverse","Muscle_Skeletal","Testis","Lung","Small_Intestine_Terminal_Ileum","Adipose_Visceral_(Omentum)","Stomach","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Pituitary","Uterus","Adipose_Subcutaneous","Brain_Nucleus_accumbens_(basal_ganglia)","Ovary","Thyroid","Brain_Spinal_cord_(cervical_c-1)","Adrenal_Gland","Brain_Substantia_nigra","Artery_Coronary","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis"],[8206,12748,14918,11417,14314,14088,11501,11746,10331,13009,9436,8893,12564,13633,13114,11607,11520,9564,8574,11406,11258,7509,7161,7132,7243,7223,8032,7577,7925,9027,8162,8745,9180,10343,9779,12253,12321,10035,13076,10610,11876,12121,12543,13267,12821,13271,12976,14659,14832],[607.721099486893,421.003422816483,352.14225540476,350.071494846365,330.560933920886,315.170023974081,232.836468030049,193.685410671219,169.69264277821,161.42441433636,126.82285002256,109.435512863401,107.691871755036,102.443170334913,84.3577408937796,78.7912920168211,77.1299680811233,65.3972759721987,0.3987924691842,-0.508629113436663,-0.514163185596864,-0.521016896570281,-0.534411120516255,-0.535927802678481,-0.536049546341605,-0.53792287654619,-0.538354673204947,-0.543907995011885,-0.545377515821566,-0.548996782042502,-0.554311457795601,-0.555830361930255,-0.56071035326444,-0.573002843378166,-0.574247640393286,-0.580659553522225,-0.581505584439339,-0.582640162573028,-0.58970079149377,-0.590701062006033,-0.600628104214785,-0.609945444110218,-0.610794976238647,-0.613506292595374,-0.617525339246145,-0.617822671679016,-0.621426461041658,-0.678307260863581,-0.681135753392188],["-4.9079<br/>[-4.9080, -4.9039]","-4.8754<br/>[-4.8756, -4.8717]","-4.8748<br/>[-4.8749, -4.8711]","-4.8764<br/>[-4.8765, -4.8727]","-4.8753<br/>[-4.8754, -4.8716]","-4.8753<br/>[-4.8754, -4.8716]","-4.8765<br/>[-4.8766, -4.8728]","-4.8764<br/>[-4.8765, -4.8727]","-5.0147<br/>[-5.0148, -5.0096]","-4.8754<br/>[-4.8755, -4.8716]","-4.8802<br/>[-4.8803, -4.8766]","-4.8774<br/>[-4.8775, -4.8738]","-4.8759<br/>[-4.8760, -4.8722]","-4.8756<br/>[-4.8757, -4.8719]","-4.8755<br/>[-4.8756, -4.8718]","-4.8760<br/>[-4.8761, -4.8723]","-4.8760<br/>[-4.8761, -4.8723]","-4.9376<br/>[-4.9378, -4.9336]","-4.8782<br/>[-4.8783, -4.8745]","-4.9399<br/>[-4.9400, -4.9356]","-4.8766<br/>[-4.8767, -4.8728]","-4.8775<br/>[-4.8776, -4.8738]","-4.8775<br/>[-4.8776, -4.8738]","-4.8775<br/>[-4.8776, -4.8738]","-4.8775<br/>[-4.8776, -4.8737]","-4.8774<br/>[-4.8776, -4.8737]","-4.8773<br/>[-4.8774, -4.8735]","-4.8773<br/>[-4.8774, -4.8736]","-4.8772<br/>[-4.8773, -4.8735]","-4.8769<br/>[-4.8770, -4.8732]","-4.8771<br/>[-4.8772, -4.8734]","-4.8770<br/>[-4.8771, -4.8732]","-4.8768<br/>[-4.8769, -4.8731]","-4.8764<br/>[-4.8765, -4.8727]","-4.8765<br/>[-4.8766, -4.8728]","-4.8759<br/>[-4.8761, -4.8722]","-4.8759<br/>[-4.8760, -4.8722]","-4.8764<br/>[-4.8765, -4.8727]","-4.9389<br/>[-4.9390, -4.9346]","-4.8762<br/>[-4.8763, -4.8724]","-4.8758<br/>[-4.8759, -4.8721]","-4.8756<br/>[-4.8757, -4.8719]","-4.8755<br/>[-4.8756, -4.8718]","-4.8753<br/>[-4.8754, -4.8716]","-4.8753<br/>[-4.8754, -4.8716]","-4.8752<br/>[-4.8753, -4.8715]","-4.8753<br/>[-4.8754, -4.8715]","-4.9389<br/>[-4.9390, -4.9346]","-4.9388<br/>[-4.9389, -4.9346]"],["-2.9423<br/>[-2.9425, -2.9417]","-3.0827<br/>[-3.2221, -3.0823]","-3.8705<br/>[-3.8715, -3.8684]","-2.6214<br/>[-2.6222, -2.6214]","-2.7980<br/>[-2.8298, -2.7963]","-2.8142<br/>[-2.8157, -2.8142]","-2.4064<br/>[-2.4064, -2.4063]","-2.3956<br/>[-2.4188, -2.3936]","-3.3967<br/>[-3.4106, -3.3811]","-3.0791<br/>[-3.0831, -3.0791]","-2.0410<br/>[-2.0469, -2.0410]","-3.4500<br/>[-3.4686, -3.4282]","-2.7029<br/>[-2.7029, -2.7029]","-2.3138<br/>[-2.3138, -2.3137]","-3.8006<br/>[-3.8155, -3.7784]","-2.3715<br/>[-2.3715, -2.3713]","-2.3649<br/>[-2.3686, -2.3649]","-3.2434<br/>[-3.2516, -3.2257]","-3.7206<br/>[-4.2183, -3.5405]","-3.7458<br/>[-3.7522, -3.7364]","-4.6396<br/>[-5.2924, -4.2609]","-5.0032<br/>[-5.8734, -4.4772]","-5.4309<br/>[-6.4235, -4.8675]","-5.5259<br/>[-6.5264, -4.9561]","-5.4385<br/>[-6.4276, -4.8712]","-5.5451<br/>[-6.5411, -4.9703]","-5.1424<br/>[-6.0818, -4.5843]","-5.5299<br/>[-6.5107, -4.9615]","-5.3587<br/>[-6.3093, -4.7957]","-5.1039<br/>[-5.9263, -4.5926]","-5.5572<br/>[-6.5181, -4.9839]","-5.3104<br/>[-6.1822, -4.7820]","-5.2580<br/>[-6.1756, -4.7004]","-5.2113<br/>[-6.0545, -4.6834]","-5.3862<br/>[-6.3031, -4.8304]","-5.0670<br/>[-5.7326, -4.6131]","-5.0564<br/>[-5.7340, -4.6131]","-5.5608<br/>[-6.4623, -5.0054]","-3.8105<br/>[-3.8137, -3.8051]","-5.5710<br/>[-6.4562, -5.0186]","-5.3987<br/>[-6.2118, -4.8661]","-5.5778<br/>[-6.4277, -5.0255]","-5.4569<br/>[-6.2753, -4.9184]","-5.3441<br/>[-6.1272, -4.8277]","-5.5599<br/>[-6.3867, -5.0155]","-5.4339<br/>[-6.2229, -4.9046]","-5.6355<br/>[-6.4653, -5.1004]","-3.8527<br/>[-3.8595, -3.8413]","-3.8575<br/>[-3.8644, -3.8457]"]],"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":[["16","12","2","19","1","14","9","20","13","8","7","18","6","15","17","10","4","3","11","5"],[10638,7537,9306,6147,7756,9738,9943,8489,7906,10545,8583,7636,9263,8072,8853,8710,12844,10533,10765,11904],[397.191862802729,337.426441092041,302.287713350339,165.95551327606,8.04197687038415,0.659325697442968,0.0888794029928386,-0.416407283620481,-0.516191858438802,-0.528304400820596,-0.584654603220533,-0.599655470918061,-0.604046113046016,-0.631589715927639,-0.649312434602391,-0.650044680556411,-0.671472280601168,-0.677578822117896,-0.677739682588208,-0.697374573695295],["-4.8767<br/>[-4.8768, -4.8731]","-4.8776<br/>[-4.8777, -4.8739]","-4.8777<br/>[-4.8778, -4.8740]","-4.9068<br/>[-4.9069, -4.9031]","-4.8913<br/>[-4.8914, -4.8881]","-4.9082<br/>[-4.9084, -4.9044]","-4.8764<br/>[-4.8765, -4.8727]","-4.8786<br/>[-4.8787, -4.8749]","-4.8783<br/>[-4.8784, -4.8746]","-4.8771<br/>[-4.8772, -4.8734]","-4.8776<br/>[-4.8777, -4.8739]","-4.8776<br/>[-4.8777, -4.8739]","-4.8774<br/>[-4.8775, -4.8737]","-4.8772<br/>[-4.8773, -4.8735]","-4.8769<br/>[-4.8770, -4.8732]","-4.8769<br/>[-4.8770, -4.8732]","-4.9401<br/>[-4.9402, -4.9358]","-4.8762<br/>[-4.8763, -4.8725]","-4.8762<br/>[-4.8763, -4.8724]","-4.8757<br/>[-4.8758, -4.8720]"],["-3.5096<br/>[-3.5399, -3.4730]","-3.3975<br/>[-3.3994, -3.3947]","-2.6509<br/>[-2.6509, -2.6291]","-2.9219<br/>[-2.9236, -2.9208]","-2.7955<br/>[-2.8001, -2.7835]","-3.6669<br/>[-3.9653, -3.4642]","-3.9900<br/>[-4.1367, -3.9037]","-4.0928<br/>[-5.0699, -3.6436]","-4.3394<br/>[-5.2471, -3.7984]","-4.3850<br/>[-5.1719, -3.9152]","-4.6371<br/>[-5.5161, -4.1073]","-4.8242<br/>[-5.7704, -4.2775]","-4.8049<br/>[-5.3541, -4.4017]","-5.1974<br/>[-6.0989, -4.6559]","-5.3277<br/>[-6.2594, -4.7639]","-5.4130<br/>[-6.3592, -4.8421]","-3.7882<br/>[-3.7989, -3.7721]","-5.4743<br/>[-6.3657, -4.9278]","-5.3964<br/>[-6.2608, -4.8589]","-5.5644<br/>[-6.4165, -5.0192]"]],"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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