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<h1 class="title toc-ignore">Enrichment results of Crohn’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> 2018-06-30</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/26192919">“Association Analyses Identify 38 Susceptibility Loci for Inflammatory Bowel Disease and Highlight Shared Genetic Risk Across Populations” (<em>Nature Genetics</em>, 2015)</a>. The summary data file is available at <a href="https://www.ibdgenetics.org/downloads.html" class="uri">https://www.ibdgenetics.org/downloads.html</a>.</p>
</div>
<div id="analysis-results" class="section level2">
<h2>Analysis results</h2>
<p>Enrichment analyses are summarized by the following three quantities.</p>
<ul>
<li><strong>BF:</strong> Bayes factor comparing the enrichment model against the baseline model;</li>
<li><strong>Outside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “outside” the gene set;</li>
<li><strong>Inside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “inside” the gene set.</li>
</ul>
<p>The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.</p>
<div id="biological-pathways" class="section level3">
<h3>Biological pathways</h3>
<div id="htmlwidget-983860bb2d7d6ad3a872" style="width:100%;height:auto;" class="datatables html-widget"></div>
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pathway<br/>(panther, PC)","Influenza A<br/>(kegg, BioSystems)","GMCSF-mediated signaling events<br/>(pid, PC)","Opioid proenkephalin pathway<br/>(panther, PC)","Opioid Signalling<br/>(reactome, BioSystems)","Signaling by ERBB2<br/>(reactome, PC)","CXCR4-mediated signaling events<br/>(pid, PC)","DAP12 signaling<br/>(reactome, PC)","Signaling by FGFR<br/>(reactome, PC)","Endothelins<br/>(pid, BioSystems)","untitled<br/>(panther, PC)","Beta1 adrenergic receptor signaling pathway<br/>(panther, PC)","Canonical NF-kappaB pathway<br/>(pid, PC)","DAP12 interactions<br/>(reactome, PC)","PKA activation<br/>(reactome, BioSystems)","Interferon alpha/beta signaling<br/>(reactome, PC)","Adenylate cyclase inhibitory pathway<br/>(reactome, PC)","Kit Receptor Signaling Pathway<br/>(wiki, BioSystems)","PKA activation<br/>(reactome, PC)","LPA receptor mediated events<br/>(pid, BioSystems)","RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways<br/>(reactome, PC)","RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways<br/>(reactome, BioSystems)","IFN-gamma pathway<br/>(pid, PC)","Adenylate cyclase inhibitory pathway<br/>(reactome, BioSystems)","Adenylate cyclase activating pathway<br/>(reactome, PC)","Gastrin-CREB signalling pathway via PKC and MAPK<br/>(reactome, BioSystems)","Glucagon signaling in metabolic regulation<br/>(reactome, PC)","PKA-mediated phosphorylation of CREB<br/>(reactome, BioSystems)","LPA receptor mediated events<br/>(pid, PC)","Thyroid hormone synthesis<br/>(kegg, BioSystems)"],[61,37,26,253,18,148,27,59,60,16,272,20,111,103,93,67,34,139,171,13,137,366,108,107,89,15,22,122,35,127,60,68,299,166,14,44,192,77,58,81,16,217,202,211,49,127,74,185,175,174,159,42,250,28,344,181,42,179,13,25,66,11,46,147,8,28,16,73,17,81,8,165,36,16,83,161,83,161,160,52,17,16,22,174,16,65,13,65,19,64,77,78,43,14,10,406,33,17,63,70],[4569,2993,2002,16422,1573,10297,1936,4435,4435,1351,21102,1868,9296,10019,9042,4490,1503,10456,12114,869,10325,26183,7929,7869,6226,980,1509,9790,1459,11032,4952,4528,29369,11135,1614,4032,13156,6501,5028,6740,1789,22534,22782,22194,3385,9493,5054,16072,19671,11609,18062,3569,19464,2226,35907,15277,4143,20403,1540,2278,4056,1207,4086,17091,889,1735,1268,6666,1839,10765,928,11504,3300,1804,10984,18025,7408,18503,18155,6722,1926,1694,2154,19201,1875,3319,1778,6664,2101,7261,5263,5283,4294,1899,1494,42311,3225,1966,7146,8822],[25.6241579282584,23.650545243979,21.472364328407,20.4064209790879,19.2701347091801,19.2603638529633,19.0937816225413,19.0182690502826,19.0182690502826,19.0044590400141,18.9201467760919,17.0173596180769,15.7037949457084,15.1361698647254,13.1993848214679,13.1544944187024,12.6130548126401,12.4364212038194,12.414836388481,12.3631408108175,12.3567612867165,12.3050484356147,12.2680810742854,12.2070219893134,12.1884425480824,12.0397092529225,11.8738471641692,11.813881066523,11.8001068865461,11.7479157035238,11.7194598792368,11.1354686039194,10.157671556936,10.0371378358223,10.0203259911167,10.0182535691772,10.0028792303782,9.86700876569157,9.82012227736485,9.81546923566113,9.6105142128878,9.5480901099939,9.53418323434908,9.52164940766915,9.4924844277667,9.4234774351116,9.39205604260701,9.31764141136182,9.28505242554375,9.22289036553408,9.20982942515891,9.15312654427452,9.0754189775775,8.89778242020177,8.8012098565141,8.70240038522155,8.66945456211914,8.65884541668797,8.65484981968605,8.52128175256057,8.33220661954356,8.29750997115971,8.2762975816866,8.24388862303364,8.17702057393892,8.17024764288519,8.1565207086835,8.06283756958143,8.06159335620985,7.99671341881113,7.97506230307208,7.95282397922014,7.93182920320444,7.93050965865109,7.8877603965113,7.84425121871,7.82907730939311,7.82247709265564,7.81748169337073,7.81459019324651,7.7630860202805,7.75031945670855,7.73504256218996,7.7336524303918,7.70501876785633,7.67426468846189,7.67368093986591,7.66642699347982,7.65908890756265,7.61540002805098,7.56918899475204,7.56491006402863,7.56008766126981,7.52568506407307,7.52378827599834,7.50482652333481,7.4895525459964,7.47547931224891,7.23065717813878,7.15236326039562],["-3.0234<br/>[-3.0234, -2.9987]","-3.0221<br/>[-3.0221, -2.9974]","-3.0199<br/>[-3.0199, -2.9953]","-3.0238<br/>[-3.0238, -2.9991]","-3.0190<br/>[-3.0190, -2.9945]","-3.0227<br/>[-3.0228, -2.9981]","-3.0193<br/>[-3.0193, -2.9948]","-3.0213<br/>[-3.0213, -2.9967]","-3.0213<br/>[-3.0213, -2.9967]","-3.0191<br/>[-3.0191, -2.9946]","-3.0232<br/>[-3.0232, -2.9986]","-3.0195<br/>[-3.0195, -2.9950]","-3.0209<br/>[-3.0209, -2.9963]","-3.0207<br/>[-3.0207, -2.9961]","-3.0206<br/>[-3.0206, -2.9960]","-3.0186<br/>[-3.0186, -2.9942]","-3.0172<br/>[-3.0172, -2.9928]","-3.0148<br/>[-3.0148, -2.9905]","-3.0209<br/>[-3.0209, -2.9963]","-3.0168<br/>[-3.0169, -2.9924]","-3.0148<br/>[-3.0148, -2.9906]","-3.0187<br/>[-3.0187, -2.9943]","-3.0148<br/>[-3.0148, -2.9905]","-3.0148<br/>[-3.0148, -2.9905]","-3.0188<br/>[-3.0188, -2.9943]","-3.0169<br/>[-3.0169, -2.9925]","-3.0171<br/>[-3.0171, -2.9926]","-3.0146<br/>[-3.0146, -2.9903]","-3.0171<br/>[-3.0171, -2.9927]","-3.0197<br/>[-3.0197, -2.9952]","-3.0185<br/>[-3.0185, -2.9940]","-3.0180<br/>[-3.0180, -2.9935]","-3.0220<br/>[-3.0220, -2.9974]","-3.0191<br/>[-3.0191, -2.9946]","-3.0163<br/>[-3.0163, -2.9920]","-3.0179<br/>[-3.0179, -2.9934]","-3.0193<br/>[-3.0193, -2.9948]","-3.0191<br/>[-3.0191, -2.9946]","-3.0180<br/>[-3.0180, -2.9936]","-3.0192<br/>[-3.0192, -2.9947]","-3.0163<br/>[-3.0163, -2.9920]","-3.0181<br/>[-3.0181, -2.9936]","-3.0201<br/>[-3.0201, -2.9955]","-3.0181<br/>[-3.0181, -2.9936]","-3.0174<br/>[-3.0174, -2.9930]","-3.0189<br/>[-3.0189, -2.9944]","-3.0167<br/>[-3.0167, -2.9923]","-3.0185<br/>[-3.0185, -2.9940]","-3.0196<br/>[-3.0196, -2.9951]","-3.0190<br/>[-3.0190, -2.9945]","-3.0194<br/>[-3.0194, -2.9949]","-3.0173<br/>[-3.0173, -2.9929]","-3.0189<br/>[-3.0189, -2.9945]","-3.0175<br/>[-3.0175, -2.9931]","-3.0207<br/>[-3.0207, -2.9961]","-3.0193<br/>[-3.0194, -2.9948]","-3.0173<br/>[-3.0173, -2.9929]","-3.0193<br/>[-3.0193, -2.9948]","-3.0159<br/>[-3.0160, -2.9916]","-3.0169<br/>[-3.0169, -2.9925]","-3.0180<br/>[-3.0180, -2.9936]","-3.0160<br/>[-3.0160, -2.9916]","-3.0173<br/>[-3.0173, -2.9928]","-3.0187<br/>[-3.0187, -2.9942]","-3.0155<br/>[-3.0155, -2.9912]","-3.0167<br/>[-3.0167, -2.9923]","-3.0168<br/>[-3.0168, -2.9924]","-3.0181<br/>[-3.0181, -2.9936]","-3.0159<br/>[-3.0159, -2.9916]","-3.0176<br/>[-3.0176, -2.9932]","-3.0155<br/>[-3.0155, -2.9912]","-3.0189<br/>[-3.0189, -2.9944]","-3.0171<br/>[-3.0171, -2.9927]","-3.0159<br/>[-3.0159, -2.9916]","-3.0176<br/>[-3.0176, -2.9932]","-3.0186<br/>[-3.0186, -2.9941]","-3.0168<br/>[-3.0168, -2.9924]","-3.0186<br/>[-3.0186, -2.9941]","-3.0186<br/>[-3.0186, -2.9941]","-3.0168<br/>[-3.0168, -2.9924]","-3.0159<br/>[-3.0159, -2.9916]","-3.0159<br/>[-3.0159, -2.9916]","-3.0173<br/>[-3.0173, -2.9929]","-3.0185<br/>[-3.0185, -2.9941]","-3.0157<br/>[-3.0157, -2.9914]","-3.0169<br/>[-3.0169, -2.9925]","-3.0157<br/>[-3.0157, -2.9914]","-3.0180<br/>[-3.0180, -2.9936]","-3.0158<br/>[-3.0158, -2.9914]","-3.0165<br/>[-3.0165, -2.9921]","-3.0172<br/>[-3.0172, -2.9928]","-3.0172<br/>[-3.0172, -2.9928]","-3.0174<br/>[-3.0174, -2.9930]","-3.0157<br/>[-3.0157, -2.9914]","-3.0157<br/>[-3.0157, -2.9914]","-3.0196<br/>[-3.0196, -2.9951]","-3.0161<br/>[-3.0161, -2.9918]","-3.0157<br/>[-3.0157, -2.9914]","-3.0165<br/>[-3.0165, -2.9921]","-3.0157<br/>[-3.0157, -2.9914]"],["-1.6255<br/>[-1.7231, -1.5464]","-1.5602<br/>[-1.6659, -1.4131]","-1.4356<br/>[-1.4563, -1.3759]","-2.0291<br/>[-2.1888, -1.9488]","-1.4265<br/>[-1.4689, -1.3623]","-1.9439<br/>[-2.0967, -1.8497]","-1.4495<br/>[-1.4697, -1.3823]","-1.7442<br/>[-1.8510, -1.6423]","-1.7442<br/>[-1.8510, -1.6423]","-1.4247<br/>[-1.4733, -1.3544]","-2.1143<br/>[-2.1851, -2.0614]","-1.4766<br/>[-1.5959, -1.4117]","-2.0074<br/>[-2.1460, -1.8726]","-2.0631<br/>[-2.1701, -1.9989]","-2.0130<br/>[-2.1407, -1.9047]","-1.7712<br/>[-1.9133, -1.6575]","-1.4716<br/>[-1.5081, -1.4006]","-2.4736<br/>[-2.5801, -2.3725]","-2.1707<br/>[-2.2552, -2.0833]","-1.3418<br/>[-1.5942, -1.1981]","-2.4008<br/>[-2.4831, -2.3089]","-2.3289<br/>[-2.4318, -2.2539]","-2.4300<br/>[-2.5330, -2.3400]","-2.4204<br/>[-2.5164, -2.3312]","-1.9045<br/>[-2.0416, -1.8194]","-1.4090<br/>[-1.6601, -1.2488]","-1.6203<br/>[-1.7656, -1.5347]","-2.4260<br/>[-2.5134, -2.3200]","-1.4851<br/>[-1.5201, -1.4058]","-2.0175<br/>[-2.1550, -1.9234]","-1.9125<br/>[-2.0658, -1.8025]","-1.8773<br/>[-2.0499, -1.7245]","-2.3103<br/>[-2.4308, -2.2139]","-2.0813<br/>[-2.1738, -2.0057]","-1.7072<br/>[-1.7686, -1.6075]","-1.9330<br/>[-2.0978, -1.8172]","-2.1072<br/>[-2.2120, -2.0223]","-1.9790<br/>[-2.1149, -1.8729]","-1.9936<br/>[-2.1689, -1.8730]","-1.9919<br/>[-2.1427, -1.8898]","-1.7337<br/>[-1.7833, -1.6121]","-2.3581<br/>[-2.4290, -2.2691]","-2.2584<br/>[-2.2883, -2.2213]","-2.3581<br/>[-2.4287, -2.2693]","-1.7985<br/>[-1.9829, -1.6795]","-2.1490<br/>[-2.2711, -2.0398]","-2.1200<br/>[-2.2358, -2.0598]","-2.2474<br/>[-2.2748, -2.1713]","-2.2656<br/>[-2.2752, -2.1696]","-2.1917<br/>[-2.3118, -2.1027]","-2.2781<br/>[-2.3143, -2.2704]","-1.8439<br/>[-2.0030, -1.7298]","-2.1900<br/>[-2.2866, -2.1307]","-1.7261<br/>[-1.8849, -1.5147]","-2.3178<br/>[-2.3178, -2.3094]","-2.1902<br/>[-2.3209, -2.0814]","-1.9720<br/>[-2.1428, -1.8408]","-2.2692<br/>[-2.2820, -2.1755]","-1.7289<br/>[-1.7827, -1.5783]","-1.8398<br/>[-2.0353, -1.7096]","-2.0350<br/>[-2.1890, -1.9461]","-1.7091<br/>[-1.7692, -1.5615]","-1.9065<br/>[-2.0651, -1.7888]","-2.2699<br/>[-2.2841, -2.1790]","-1.6673<br/>[-1.7468, -1.5238]","-1.7935<br/>[-1.9757, -1.5198]","-1.5488<br/>[-1.7304, -1.4215]","-2.0202<br/>[-2.1853, -1.9093]","-1.7762<br/>[-2.0229, -1.6761]","-2.1490<br/>[-2.2024, -2.1396]","-1.6837<br/>[-1.7572, -1.5622]","-2.2256<br/>[-2.3417, -2.1764]","-1.7743<br/>[-1.9583, -1.6726]","-1.7837<br/>[-2.0246, -1.6794]","-2.1513<br/>[-2.2115, -2.1411]","-2.2895<br/>[-2.3326, -2.2890]","-2.2374<br/>[-2.4903, -2.1051]","-2.2768<br/>[-2.2903, -2.2067]","-2.2902<br/>[-2.3332, -2.2896]","-2.1248<br/>[-2.1328, -2.1188]","-1.8007<br/>[-2.0342, -1.6908]","-1.7937<br/>[-2.0253, -1.6849]","-1.7208<br/>[-1.9155, -1.5131]","-2.3247<br/>[-2.3616, -2.2872]","-1.8002<br/>[-2.0322, -1.6937]","-1.8449<br/>[-2.0504, -1.7179]","-1.7821<br/>[-2.0269, -1.6838]","-2.1129<br/>[-2.3066, -1.9819]","-1.8142<br/>[-2.0365, -1.7084]","-2.1688<br/>[-2.2709, -2.1327]","-1.9954<br/>[-2.1657, -1.8797]","-1.9959<br/>[-2.1661, -1.8797]","-1.9288<br/>[-2.0959, -1.8076]","-1.8106<br/>[-2.0369, -1.7039]","-1.7697<br/>[-2.0221, -1.6718]","-2.4459<br/>[-2.4917, -2.3792]","-1.9869<br/>[-2.0861, -1.7662]","-1.8258<br/>[-2.0598, -1.7150]","-2.1724<br/>[-2.2691, -2.1318]","-2.1859<br/>[-2.3170, -2.1642]"]],"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":[["Testis","Pituitary","Brain - Cerebellum","Brain - Cerebellar Hemisphere","Stomach","Ovary","Adrenal Gland","Esophagus - Gastroesophageal Junction","Prostate","Colon - Sigmoid","Brain - Anterior cingulate cortex (BA24)","Esophagus - Muscularis","Uterus","Thyroid","Artery - Coronary","Vagina","Adipose - Subcutaneous","Artery - Tibial","Muscle - Skeletal","Adipose - Visceral (Omentum)","Heart - Atrial Appendage","Brain - Cortex","Heart - Left Ventricle","Artery - Aorta","Colon - Transverse","Cells - EBV-transformed lymphocytes","Pancreas","Breast - Mammary Tissue","Lung","Nerve - Tibial","Brain - Frontal Cortex (BA9)","Skin - Not Sun Exposed (Suprapubic)","Small Intestine - Terminal Ileum","Brain - Nucleus accumbens (basal ganglia)","Brain - Caudate (basal ganglia)","Brain - Hypothalamus","Skin - Sun Exposed (Lower leg)","Whole Blood","Spleen","Cells - Transformed fibroblasts","Esophagus - Mucosa","Brain - Putamen (basal ganglia)","Brain - Hippocampus","Liver"],[5827,5876,5545,5520,5334,5928,5598,5840,5621,5940,5751,5973,5723,6195,6125,5790,5560,6006,5690,5715,5636,5644,5616,6357,5360,5133,5175,5549,4862,5599,6032,5850,4704,6066,6396,5775,5837,5645,3970,6140,5672,6486,5633,6320],[1.32936726108927,1.133783691011,1.06555938623694,0.80858900909379,0.774127769116707,0.567616171579653,0.50098946286293,0.4470183660424,0.388272399986032,0.368444641159429,0.2990772219502,0.255334350831108,0.192333437034182,0.179880106791065,0.148841610072584,0.0921334564580597,0.0604972976751933,-0.000751884382044104,-0.0162740998807076,-0.0379816151647041,-0.0394593547865587,-0.120945885152376,-0.125510682796968,-0.158124910321327,-0.17726915374479,-0.187825068464372,-0.217444813383675,-0.244054728038599,-0.253184280881181,-0.260433530544524,-0.332171090729911,-0.362832070512161,-0.390955528078919,-0.434776402097364,-0.43536274468981,-0.460213314661631,-0.473912247818521,-0.521824932825637,-0.580017050313001,-0.582135863486451,-0.703202414211962,-0.728148828675205,-0.776267186575981,-0.993896849622585],["-3.0158<br/>[-3.0158, -2.9914]","-3.0156<br/>[-3.0156, -2.9913]","-3.0154<br/>[-3.0154, -2.9911]","-3.0154<br/>[-3.0154, -2.9911]","-3.0153<br/>[-3.0153, -2.9910]","-3.0151<br/>[-3.0151, -2.9908]","-3.0148<br/>[-3.0148, -2.9905]","-3.0150<br/>[-3.0150, -2.9907]","-3.0154<br/>[-3.0154, -2.9911]","-3.0150<br/>[-3.0150, -2.9907]","-3.0152<br/>[-3.0152, -2.9909]","-3.0150<br/>[-3.0150, -2.9907]","-3.0153<br/>[-3.0153, -2.9910]","-3.0147<br/>[-3.0147, -2.9904]","-3.0149<br/>[-3.0149, -2.9906]","-3.0149<br/>[-3.0149, -2.9906]","-3.0148<br/>[-3.0149, -2.9905]","-3.0149<br/>[-3.0149, -2.9906]","-3.0147<br/>[-3.0147, -2.9904]","-3.0148<br/>[-3.0149, -2.9906]","-3.0146<br/>[-3.0146, -2.9904]","-3.0147<br/>[-3.0148, -2.9905]","-3.0146<br/>[-3.0146, -2.9903]","-3.0150<br/>[-3.0150, -2.9907]","-3.0149<br/>[-3.0149, -2.9906]","-3.0151<br/>[-3.0151, -2.9908]","-3.0151<br/>[-3.0151, -2.9908]","-3.0147<br/>[-3.0147, -2.9904]","-3.0147<br/>[-3.0147, -2.9904]","-3.0146<br/>[-3.0147, -2.9904]","-3.0147<br/>[-3.0147, -2.9904]","-3.0150<br/>[-3.0150, -2.9907]","-3.0146<br/>[-3.0146, -2.9903]","-3.0147<br/>[-3.0147, -2.9904]","-3.0147<br/>[-3.0147, -2.9904]","-3.0148<br/>[-3.0148, -2.9905]","-3.0150<br/>[-3.0150, -2.9906]","-3.0146<br/>[-3.0146, -2.9903]","-3.0146<br/>[-3.0146, -2.9904]","-3.0147<br/>[-3.0147, -2.9904]","-3.0146<br/>[-3.0146, -2.9903]","-3.0143<br/>[-3.0143, -2.9900]","-3.0144<br/>[-3.0144, -2.9901]","-3.0141<br/>[-3.0141, -2.9899]"],["-2.2782<br/>[-2.5800, -2.0812]","-2.3161<br/>[-2.6453, -2.1237]","-2.2934<br/>[-2.6501, -2.0940]","-2.3506<br/>[-2.7226, -2.1553]","-2.3019<br/>[-2.7596, -2.1060]","-2.4068<br/>[-2.7833, -2.2141]","-2.3975<br/>[-2.7911, -2.1996]","-2.3819<br/>[-2.8092, -2.1802]","-2.3928<br/>[-2.7981, -2.1841]","-2.3991<br/>[-2.8254, -2.1951]","-2.4268<br/>[-2.8113, -2.2132]","-2.4238<br/>[-2.8219, -2.2118]","-2.4329<br/>[-2.8229, -2.2146]","-2.4686<br/>[-2.8305, -2.2580]","-2.4458<br/>[-2.8320, -2.2264]","-2.4627<br/>[-2.8273, -2.2454]","-2.4617<br/>[-2.8376, -2.2442]","-2.4838<br/>[-2.8594, -2.2714]","-2.5135<br/>[-2.8378, -2.2973]","-2.4923<br/>[-2.8531, -2.2599]","-2.5095<br/>[-2.8504, -2.2925]","-2.5021<br/>[-2.8679, -2.2599]","-2.5356<br/>[-2.8468, -2.3118]","-2.5005<br/>[-2.8972, -2.2686]","-2.4939<br/>[-2.8863, -2.2585]","-2.5258<br/>[-2.8705, -2.2947]","-2.5388<br/>[-2.8727, -2.3109]","-2.5476<br/>[-2.8810, -2.3087]","-2.5368<br/>[-2.8738, -2.2952]","-2.5499<br/>[-2.8849, -2.3076]","-2.5765<br/>[-2.9014, -2.3375]","-2.5936<br/>[-2.8966, -2.3574]","-2.5876<br/>[-2.8851, -2.3475]","-2.6080<br/>[-2.9170, -2.3689]","-2.6097<br/>[-2.9204, -2.3675]","-2.5974<br/>[-2.9287, -2.3372]","-2.6339<br/>[-2.9084, -2.4057]","-2.6037<br/>[-2.9513, -2.3356]","-2.6305<br/>[-2.9336, -2.3680]","-2.6526<br/>[-2.9446, -2.4007]","-2.7019<br/>[-2.9622, -2.4540]","-2.7058<br/>[-2.9783, -2.4471]","-2.7112<br/>[-2.9998, -2.4327]","-2.8393<br/>[-3.0427, -2.5925]"]],"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","Brain_Frontal_Cortex_(BA9)","Cells_EBV-transformed_lymphocytes","Minor_Salivary_Gland","Spleen","Stomach","Colon_Sigmoid","Lung","Colon_Transverse","Brain_Hippocampus","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Cortex","Brain_Caudate_(basal_ganglia)","Whole_Blood","Artery_Tibial","Brain_Putamen_(basal_ganglia)","Brain_Amygdala","Adipose_Visceral_(Omentum)","Kidney_Cortex","Brain_Hypothalamus","Small_Intestine_Terminal_Ileum","Uterus","Artery_Coronary","Brain_Cerebellum","Liver","Muscle_Skeletal","Esophagus_Muscularis","Skin_Not_Sun_Exposed_(Suprapubic)","Brain_Nucleus_accumbens_(basal_ganglia)","Nerve_Tibial","Cells_Transformed_fibroblasts","Skin_Sun_Exposed_(Lower_leg)","Pituitary","Artery_Aorta","Esophagus_Gastroesophageal_Junction","Prostate","Brain_Cerebellar_Hemisphere","Heart_Left_Ventricle","Heart_Atrial_Appendage","Pancreas","Thyroid","Vagina","Breast_Mammary_Tissue","Esophagus_Mucosa","Adrenal_Gland","Adipose_Subcutaneous","Brain_Substantia_nigra","Ovary","Brain_Spinal_cord_(cervical_c-1)"],[8073,13193,7577,8261,6947,9142,10574,8033,7694,10682,12624,11617,11545,6761,12432,11600,10930,9266,8970,11843,8663,11953,12045,10581,8399,8606,13955,6785,11125,12183,10791,6683,9317,14085,13793,9136,13212,10900,10954,7638,11909,6785,9609,6846,12354,9699,12333,11300,12222],[2.44586498953197,1.25127979116061,0.764582273373052,0.285893046248539,0.214665894141974,0.0234407429714176,0.0224649646713924,-0.0246663552947255,-0.128309421270223,-0.187129088429955,-0.286753156950009,-0.416781991204494,-0.51832554722187,-0.535401531641211,-0.543433775433285,-0.546936338855606,-0.584597011132537,-0.611634384535736,-0.626288949951438,-0.647426944708438,-0.674209733592505,-0.698585437108716,-0.789232459119232,-0.793727435012514,-0.825051372437137,-0.859143852219857,-0.860821168071853,-0.875339544940178,-0.883127044611551,-0.913838964318507,-0.92325907062834,-0.933897635733374,-0.960736643762139,-0.963161100246339,-0.978851410110158,-0.98191119357094,-0.98322489071562,-0.984661609652738,-1.01037434096764,-1.05933315903137,-1.09853919210887,-1.10431167020217,-1.13366724728417,-1.13813241068745,-1.18761589856123,-1.19033846290038,-1.22883588094298,-1.28612621644055,-1.31889866144664],["-3.0167<br/>[-3.0167, -2.9923]","-3.0153<br/>[-3.0153, -2.9910]","-3.0155<br/>[-3.0155, -2.9911]","-3.0157<br/>[-3.0157, -2.9914]","-3.0152<br/>[-3.0152, -2.9909]","-3.0156<br/>[-3.0156, -2.9912]","-3.0158<br/>[-3.0158, -2.9914]","-3.0152<br/>[-3.0152, -2.9909]","-3.0149<br/>[-3.0149, -2.9906]","-3.0149<br/>[-3.0149, -2.9906]","-3.0150<br/>[-3.0150, -2.9907]","-3.0147<br/>[-3.0147, -2.9904]","-3.0141<br/>[-3.0141, -2.9898]","-3.0147<br/>[-3.0147, -2.9904]","-3.0147<br/>[-3.0147, -2.9904]","-3.0141<br/>[-3.0141, -2.9898]","-3.0145<br/>[-3.0145, -2.9902]","-3.0150<br/>[-3.0150, -2.9907]","-3.0149<br/>[-3.0149, -2.9906]","-3.0144<br/>[-3.0144, -2.9901]","-3.0144<br/>[-3.0144, -2.9902]","-3.0148<br/>[-3.0148, -2.9904]","-3.0145<br/>[-3.0145, -2.9903]","-3.0144<br/>[-3.0144, -2.9901]","-3.0145<br/>[-3.0145, -2.9902]","-3.0141<br/>[-3.0141, -2.9898]","-3.0146<br/>[-3.0147, -2.9903]","-3.0141<br/>[-3.0141, -2.9899]","-3.0141<br/>[-3.0141, -2.9898]","-3.0142<br/>[-3.0142, -2.9900]","-3.0146<br/>[-3.0146, -2.9903]","-3.0141<br/>[-3.0141, -2.9898]","-3.0144<br/>[-3.0144, -2.9901]","-3.0143<br/>[-3.0143, -2.9901]","-3.0144<br/>[-3.0144, -2.9900]","-3.0140<br/>[-3.0140, -2.9898]","-3.0142<br/>[-3.0142, -2.9899]","-3.0144<br/>[-3.0144, -2.9901]","-3.0143<br/>[-3.0143, -2.9901]","-3.0141<br/>[-3.0141, -2.9899]","-3.0143<br/>[-3.0143, -2.9900]","-3.0141<br/>[-3.0141, -2.9898]","-3.0140<br/>[-3.0140, -2.9897]","-3.0139<br/>[-3.0139, -2.9897]","-3.0139<br/>[-3.0139, -2.9896]","-3.0139<br/>[-3.0139, -2.9897]","-3.0139<br/>[-3.0139, -2.9896]","-3.0136<br/>[-3.0136, -2.9894]","-3.0136<br/>[-3.0136, -2.9894]"],["-2.3295<br/>[-2.5215, -2.1818]","-2.5081<br/>[-2.5975, -2.3830]","-2.3995<br/>[-2.7469, -2.2116]","-2.4770<br/>[-2.8357, -2.3115]","-2.4634<br/>[-2.8140, -2.2736]","-2.5580<br/>[-2.8684, -2.3629]","-2.5908<br/>[-2.8855, -2.4171]","-2.5542<br/>[-2.8739, -2.3610]","-2.5658<br/>[-2.8819, -2.3636]","-2.6191<br/>[-2.9022, -2.4355]","-2.6633<br/>[-2.9102, -2.4817]","-2.6786<br/>[-2.9230, -2.4844]","-2.7041<br/>[-2.9324, -2.5155]","-2.6159<br/>[-2.9075, -2.3988]","-2.6907<br/>[-2.9453, -2.4933]","-2.7107<br/>[-2.9359, -2.5167]","-2.7195<br/>[-2.9357, -2.5328]","-2.7062<br/>[-2.9435, -2.5025]","-2.7062<br/>[-2.9472, -2.4897]","-2.7370<br/>[-2.9457, -2.5458]","-2.7124<br/>[-2.9585, -2.4883]","-2.7289<br/>[-2.9607, -2.5250]","-2.7550<br/>[-2.9734, -2.5424]","-2.7630<br/>[-2.9764, -2.5490]","-2.7738<br/>[-2.9756, -2.5504]","-2.7797<br/>[-2.9817, -2.5578]","-2.7868<br/>[-2.9786, -2.5868]","-2.7899<br/>[-2.9922, -2.5690]","-2.8023<br/>[-2.9827, -2.6129]","-2.8099<br/>[-2.9890, -2.6100]","-2.8122<br/>[-2.9923, -2.6139]","-2.8178<br/>[-3.0073, -2.5921]","-2.8274<br/>[-3.0037, -2.6237]","-2.8175<br/>[-2.9953, -2.6186]","-2.8284<br/>[-2.9927, -2.6382]","-2.8353<br/>[-3.0090, -2.6256]","-2.8329<br/>[-3.0026, -2.6397]","-2.8343<br/>[-3.0054, -2.6324]","-2.8453<br/>[-3.0095, -2.6494]","-2.8691<br/>[-3.0492, -2.6502]","-2.8825<br/>[-3.0228, -2.7015]","-2.9038<br/>[-3.0729, -2.6843]","-2.9028<br/>[-3.0489, -2.7139]","-2.9258<br/>[-3.0848, -2.7086]","-2.9189<br/>[-3.0438, -2.7412]","-2.9320<br/>[-3.0656, -2.7399]","-2.9350<br/>[-3.0596, -2.7570]","-2.9728<br/>[-3.0841, -2.8084]","-2.9824<br/>[-3.0897, -2.8216]"]],"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":[["1","16","13","17","2","3","10","12","5","4","6","9","15","7","19","8","20","18","11","14"],[7284,9832,7690,8015,8803,9868,8327,7154,11214,12138,8755,9549,7646,8403,5732,10277,7956,7381,10315,9312],[15.3738299733312,3.4591981587893,2.0378363268881,1.66710339482469,0.653857037805455,0.453805085231818,0.331680998474073,0.288865559578258,0.166040757127546,0.0192375455421287,-0.273885371093804,-0.390483988783124,-0.435028142092475,-0.475640342636804,-0.493249532764797,-0.553242059285586,-0.633305293221237,-0.668746733645908,-0.735747413409952,-0.744153414580006],["-3.0158<br/>[-3.0158, -2.9915]","-3.0166<br/>[-3.0166, -2.9920]","-3.0156<br/>[-3.0156, -2.9913]","-3.0162<br/>[-3.0162, -2.9919]","-3.0157<br/>[-3.0157, -2.9914]","-3.0148<br/>[-3.0148, -2.9905]","-3.0155<br/>[-3.0155, -2.9912]","-3.0149<br/>[-3.0149, -2.9906]","-3.0155<br/>[-3.0155, -2.9912]","-3.0145<br/>[-3.0145, -2.9903]","-3.0145<br/>[-3.0145, -2.9903]","-3.0149<br/>[-3.0149, -2.9906]","-3.0147<br/>[-3.0147, -2.9904]","-3.0143<br/>[-3.0144, -2.9901]","-3.0144<br/>[-3.0144, -2.9901]","-3.0145<br/>[-3.0145, -2.9902]","-3.0145<br/>[-3.0145, -2.9902]","-3.0146<br/>[-3.0146, -2.9903]","-3.0139<br/>[-3.0139, -2.9901]","-3.0144<br/>[-3.0144, -2.9901]"],["-2.1160<br/>[-2.1589, -2.0292]","-2.2914<br/>[-2.4965, -2.1564]","-2.3359<br/>[-2.4961, -2.1860]","-2.2971<br/>[-2.5878, -2.1206]","-2.4820<br/>[-2.8106, -2.3011]","-2.5175<br/>[-2.8576, -2.3374]","-2.5077<br/>[-2.8644, -2.3100]","-2.4712<br/>[-2.8633, -2.2330]","-2.5665<br/>[-2.8905, -2.3765]","-2.6104<br/>[-2.9050, -2.4164]","-2.6203<br/>[-2.9445, -2.3873]","-2.6903<br/>[-2.9395, -2.4759]","-2.6917<br/>[-2.9431, -2.4736]","-2.7262<br/>[-2.9357, -2.5285]","-2.6748<br/>[-2.9727, -2.4162]","-2.7370<br/>[-2.9688, -2.5257]","-2.7622<br/>[-2.9757, -2.5481]","-2.7736<br/>[-2.9847, -2.5521]","-2.8133<br/>[-2.9817, -2.6208]","-2.8089<br/>[-2.9918, -2.6006]"]],"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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