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<h1 class="title toc-ignore">Enrichment results of adult human height</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> 2018-10-05</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/25282103">“Defining the Role of Common Variation in the Genomic and Biological Architecture of Adult Human Height” (<em>Nature Genetics</em>, 2014)</a>. The summary data file is available at <a href="https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files" class="uri">https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files</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)","Metabolism of RNA<br/>(3856, reactome, PC)","HTLV-I infection<br/>(3846, kegg, BioSystems)","PI3K-Akt signaling pathway<br/>(3897, kegg, BioSystems)","Hedgehog 'on' state<br/>(3398, reactome, BioSystems)","Fc epsilon receptor (FCERI) signaling<br/>(3893, reactome, BioSystems)","IRS-related events triggered by IGF1R<br/>(3865, reactome, BioSystems)","Transcriptional misregulation in cancer<br/>(3760, kegg, BioSystems)","Adipogenesis<br/>(3667, wiki, BioSystems)","Integrated Pancreatic Cancer Pathway<br/>(3791, wiki, BioSystems)","Signaling by Insulin receptor<br/>(3873, reactome, BioSystems)","Signaling by Hedgehog<br/>(3677, reactome, BioSystems)","NGF signalling via TRKA from the plasma membrane<br/>(3898, reactome, BioSystems)","Signaling by ERBB4<br/>(3880, reactome, BioSystems)","VEGFA-VEGFR2 Pathway<br/>(3879, reactome, BioSystems)","Hemostasis<br/>(3914, reactome, PC)","Signaling by VEGF<br/>(3883, reactome, BioSystems)","Signaling by PDGF<br/>(3896, reactome, 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kegg, BioSystems)","IGF1R signaling cascade<br/>(3468, reactome, PC)","IRS-mediated signalling<br/>(3863, reactome, BioSystems)","Mitotic M-M/G1 phases<br/>(3890, reactome, PC)","Signaling by Wnt<br/>(3891, reactome, BioSystems)","Ras signaling pathway<br/>(3817, kegg, BioSystems)","B Cell Receptor Signaling Pathway<br/>(3731, wiki, BioSystems)","MAPK family signaling cascades<br/>(3862, reactome, BioSystems)","Signaling by Wnt<br/>(3887, reactome, PC)","RHO GTPase Effectors<br/>(3869, reactome, BioSystems)","Signaling pathways regulating pluripotency of stem cells<br/>(3702, kegg, BioSystems)","Signaling by Rho GTPases<br/>(3903, reactome, BioSystems)","Signaling by ERBB2<br/>(3885, reactome, BioSystems)","M Phase<br/>(3871, reactome, PC)","Diseases of signal transduction<br/>(3855, reactome, BioSystems)","GPCR ligand binding<br/>(3908, reactome, PC)","Signaling by the B Cell Receptor (BCR)<br/>(3793, reactome, BioSystems)","Signaling by WNT in cancer<br/>(3842, reactome, PC)","M Phase<br/>(3872, reactome, BioSystems)","B Cell Activation<br/>(3790, reactome, PC)","GPCR ligand binding<br/>(3909, reactome, BioSystems)","Signaling events mediated by the Hedgehog family<br/>(2045, pid, BioSystems)","Signaling events mediated by the Hedgehog family<br/>(2067, pid, PC)","Class I MHC mediated antigen processing & presentation<br/>(3854, reactome, BioSystems)","Signaling by FGFR4<br/>(3881, reactome, BioSystems)","Signaling by EGFR<br/>(3892, reactome, BioSystems)","Downstream signaling of activated FGFR4<br/>(3878, reactome, BioSystems)","Viral carcinogenesis<br/>(3799, kegg, BioSystems)","Signaling by FGFR2<br/>(3882, reactome, BioSystems)","Mitotic G1-G1/S phases<br/>(3669, reactome, PC)","Androgen receptor signaling pathway<br/>(3420, wiki, BioSystems)","Signalling to RAS<br/>(3832, reactome, BioSystems)","Antigen processing: Ubiquitination & Proteasome degradation<br/>(3812, reactome, BioSystems)","Signaling by Insulin receptor<br/>(3608, reactome, PC)","Class I MHC mediated antigen processing & presentation<br/>(3840, reactome, PC)","FoxO signaling pathway<br/>(3661, kegg, BioSystems)","DAP12 signaling<br/>(3889, reactome, BioSystems)","S Phase<br/>(3630, reactome, PC)","S Phase<br/>(3639, reactome, BioSystems)","Molecules associated with elastic fibres<br/>(2380, reactome, PC)","Hepatitis B<br/>(3709, kegg, BioSystems)","Signalling to ERKs<br/>(3836, reactome, BioSystems)","Translation<br/>(3699, reactome, BioSystems)","Prostate cancer<br/>(3441, kegg, BioSystems)","Downstream signaling events of B Cell Receptor (BCR)<br/>(3746, reactome, PC)","Hedgehog Signaling Pathway<br/>(2038, wiki, BioSystems)","Downstream signaling events of B Cell Receptor (BCR)<br/>(3750, reactome, BioSystems)","Translation<br/>(3692, reactome, PC)","TGF-beta signaling pathway<br/>(3378, kegg, BioSystems)","DAP12 interactions<br/>(3894, reactome, BioSystems)","Organelle biogenesis and maintenance<br/>(3710, reactome, PC)"],[65,366,457,463,258,183,149,147,254,259,359,410,246,385,252,241,257,250,335,83,330,271,170,130,190,292,132,344,303,302,490,309,335,298,271,496,203,313,333,41,50,195,273,311,211,442,406,87,476,55,90,268,316,318,220,153,264,312,274,138,375,311,284,256,421,191,244,288,188,426,22,23,256,304,325,301,197,307,131,84,231,213,112,242,128,315,118,121,30,142,238,137,86,163,22,164,136,80,330,143],[7573,24387,31432,31834,16444,10005,13241,13140,27448,28019,26162,42783,25117,40147,22581,15037,17586,18860,32932,6283,32021,25621,15096,12469,17485,27268,11887,34905,29159,29800,46399,30780,33892,27961,25586,46672,11365,31128,33101,4603,4377,19385,30785,25500,14412,24029,41928,7471,58142,4767,7756,25136,20814,23655,22366,16173,25128,23116,19097,11496,32907,30840,18629,24103,32984,18262,15362,18845,18077,33335,2490,2495,20181,30364,32798,30105,13863,30590,9246,7137,22070,17825,9498,19274,11400,31730,8468,8643,3418,11920,22881,9419,8149,15125,1800,15131,9416,6621,32565,11198],[68.8862016133663,64.3610613582384,60.2486186803681,59.7100882117568,54.5693688973819,49.4832435204049,48.8143837349395,48.7957551697753,48.4813176388026,48.4292324810719,47.192881516199,46.863880362955,46.2020160320493,45.8613924008229,45.3633885191687,45.3314209001459,43.9000313025381,42.1230163323821,41.2758073371355,40.2865720861261,39.8676031706658,39.7317215182171,39.293539326958,38.9067746763615,38.8330085774341,38.2571331725315,37.9308648214284,37.7048561004853,37.2290254647025,37.1321013568989,36.8071205148252,36.8005485343511,36.6512280778931,36.5421494109434,36.5418282905122,36.4444980069655,36.1243642163309,35.9139861083397,35.8346989503635,35.691951898713,35.6699503888098,35.5601492569533,35.4031770948915,35.4015455357779,35.0779728766463,35.0145369654243,34.7330358824933,34.6767843113591,34.510292642504,34.1098987487604,33.9766099235721,33.9267429111293,33.8440226420421,33.6091472904146,33.4806555041672,33.4340670155549,32.8187556034526,32.807225307214,32.7699488899132,32.363661299432,32.2686409299567,32.0226565400787,31.344773316669,31.2228382549267,31.2214666052147,31.0951313721818,31.0215374517961,31.0033669151105,30.9596070122248,30.7320757901699,30.6150775428271,30.4185498318495,30.3703097939564,30.1086231869801,30.0550614338482,30.015879257638,29.9131798631345,29.7269944288292,29.7145183065645,29.5801385574068,28.5356640553806,28.3756661437539,28.2776635415764,28.2032100157037,28.1838851097996,27.8226497645863,27.7156163354568,27.6633229414919,27.4576273365842,27.4532392299086,27.204816359787,26.7443321225499,26.7235892532488,26.7128310592725,26.7002508207139,26.6876590302971,26.5796551424261,26.3651920404217,26.2743797248527,25.3671081181942],["-1.9687<br/>[-2.0066, 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-1.5789]","-1.5138<br/>[-1.5140, -1.5076]","-1.4759<br/>[-1.4819, -1.4632]","-1.4854<br/>[-1.5162, -1.4505]","-1.5333<br/>[-1.5963, -1.4866]","-1.6164<br/>[-1.6527, -1.5783]","-1.4416<br/>[-1.4470, -1.4176]","-1.5719<br/>[-1.6276, -1.5373]","-1.6045<br/>[-1.6469, -1.5784]","-1.6243<br/>[-1.6676, -1.5991]","-1.7080<br/>[-1.7306, -1.6748]","-1.6296<br/>[-1.6698, -1.6010]","-1.6248<br/>[-1.6610, -1.5917]","-1.5794<br/>[-1.6193, -1.5269]","-1.6128<br/>[-1.6576, -1.5786]","-1.6985<br/>[-1.7371, -1.6752]","-1.4607<br/>[-1.5066, -1.4321]","-1.6167<br/>[-1.6508, -1.5886]","-1.6907<br/>[-1.7000, -1.6703]","-1.3266<br/>[-1.3698, -1.2865]","-1.2613<br/>[-1.3317, -1.2463]","-1.4996<br/>[-1.5037, -1.4865]","-1.6279<br/>[-1.6546, -1.5942]","-1.5796<br/>[-1.5985, -1.5577]","-1.4972<br/>[-1.5435, -1.4650]","-1.6250<br/>[-1.6536, -1.6049]","-1.6915<br/>[-1.7256, -1.6628]","-1.3858<br/>[-1.4237, -1.3474]","-1.7446<br/>[-1.7738, -1.7026]","-1.2820<br/>[-1.3071, -1.2487]","-1.3961<br/>[-1.4284, -1.3569]","-1.6220<br/>[-1.6612, -1.5869]","-1.5923<br/>[-1.6362, -1.5519]","-1.5965<br/>[-1.6351, -1.5670]","-1.6031<br/>[-1.6492, -1.5809]","-1.5581<br/>[-1.5951, -1.5241]","-1.6144<br/>[-1.6538, -1.5794]","-1.5971<br/>[-1.6352, -1.5671]","-1.6204<br/>[-1.6640, -1.5752]","-1.4429<br/>[-1.4772, -1.4014]","-1.7080<br/>[-1.7349, -1.6744]","-1.6188<br/>[-1.6634, -1.5475]","-1.6157<br/>[-1.6530, -1.5571]","-1.5851<br/>[-1.6110, -1.5673]","-1.6895<br/>[-1.7239, -1.6615]","-1.5575<br/>[-1.5785, -1.5112]","-1.5594<br/>[-1.5922, -1.5189]","-1.6047<br/>[-1.6537, -1.5470]","-1.5550<br/>[-1.5782, -1.5241]","-1.6931<br/>[-1.7204, -1.6616]","-1.2094<br/>[-1.2532, -1.1515]","-1.2096<br/>[-1.2631, -1.1335]","-1.5904<br/>[-1.6315, -1.5599]","-1.5681<br/>[-1.6590, -1.5423]","-1.5976<br/>[-1.6748, -1.5520]","-1.5668<br/>[-1.6521, -1.5421]","-1.5312<br/>[-1.5810, -1.4929]","-1.5720<br/>[-1.6593, -1.5431]","-1.4332<br/>[-1.4891, -1.3695]","-1.4151<br/>[-1.4752, -1.3724]","-1.5696<br/>[-1.6491, -1.5250]","-1.5817<br/>[-1.6222, -1.5507]","-1.4789<br/>[-1.5297, -1.4411]","-1.5949<br/>[-1.6335, -1.5618]","-1.4485<br/>[-1.4960, -1.4164]","-1.5901<br/>[-1.6708, -1.5534]","-1.4293<br/>[-1.4719, -1.3895]","-1.4328<br/>[-1.4734, -1.3907]","-1.3310<br/>[-1.3865, -1.2890]","-1.4717<br/>[-1.5241, -1.4281]","-1.6161<br/>[-1.6661, -1.5563]","-1.4000<br/>[-1.4651, -1.3657]","-1.3951<br/>[-1.4576, -1.3660]","-1.4863<br/>[-1.5571, -1.4435]","-1.2007<br/>[-1.2335, -1.1889]","-1.4853<br/>[-1.5571, -1.4435]","-1.3999<br/>[-1.4699, -1.3594]","-1.4042<br/>[-1.4519, -1.3647]","-1.6080<br/>[-1.6807, -1.5565]","-1.5353<br/>[-1.5829, -1.4883]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(ID, 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":[["Artery - Aorta","Artery - Coronary","Pituitary","Artery - Tibial","Esophagus - Muscularis","Colon - Sigmoid","Esophagus - Gastroesophageal Junction","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Nerve - Tibial","Ovary","Prostate","Uterus","Skin - Not Sun Exposed (Suprapubic)","Breast - Mammary Tissue","Thyroid","Colon - Transverse","Adrenal Gland","Cells - Transformed fibroblasts","Stomach","Brain - Caudate (basal ganglia)","Brain - Cerebellum","Brain - Hippocampus","Cells - EBV-transformed lymphocytes","Brain - Hypothalamus","Brain - Putamen (basal ganglia)","Brain - Cerebellar Hemisphere","Pancreas","Vagina","Brain - Cortex","Lung","Brain - Nucleus accumbens (basal ganglia)","Liver","Muscle - Skeletal","Brain - Anterior cingulate cortex (BA24)","Testis","Brain - Frontal Cortex (BA9)","Skin - Sun Exposed (Lower leg)","Spleen","Esophagus - Mucosa","Small Intestine - Terminal Ileum","Heart - Left Ventricle","Heart - Atrial Appendage","Whole Blood"],[6517,6308,5553,6228,6018,5928,5817,5599,5737,5622,5728,5559,5632,5798,5454,6001,5192,5351,6073,5151,5945,5591,5493,4878,5519,6156,5762,5192,5717,5694,5079,5865,6487,5707,5786,5637,6156,5727,3821,5512,4748,5535,5547,5801],[20.9468184316883,14.4649597187659,13.5941510402003,13.1118848194883,13.0148183928349,11.7796225165304,11.3260358606895,11.1700670583592,9.09820661481993,8.99042640605908,8.68003884477149,8.52878493538681,8.4867755718057,8.34434578354722,8.19092848683128,7.65907559707973,6.81650585007826,6.69446979201861,6.5881687208051,6.0332216756551,6.00940472287845,5.58205377033169,5.35291549451701,5.33125506078197,5.14817051160825,5.13229750980688,4.65408342295365,4.30703688687621,4.30599693448932,4.25155303972393,4.2342913895442,3.9073199075845,3.82522569305536,3.76984069552096,3.55547150972297,3.31386280222122,3.02970396480579,2.55205261513189,2.05162452049783,1.83543710695662,1.50496445691981,1.46153234266814,1.38344249560351,0.422808231813606],["-1.9666<br/>[-2.0044, -1.9621]","-1.9662<br/>[-2.0040, -1.9617]","-1.9661<br/>[-2.0038, -1.9615]","-1.9662<br/>[-2.0039, -1.9616]","-1.9660<br/>[-2.0038, -1.9615]","-1.9659<br/>[-2.0036, -1.9614]","-1.9659<br/>[-2.0037, -1.9614]","-1.9659<br/>[-2.0036, -1.9614]","-1.9657<br/>[-2.0035, -1.9612]","-1.9657<br/>[-2.0034, -1.9612]","-1.9659<br/>[-2.0036, -1.9614]","-1.9657<br/>[-2.0034, -1.9612]","-1.9657<br/>[-2.0034, -1.9612]","-1.9656<br/>[-2.0033, -1.9611]","-1.9657<br/>[-2.0034, -1.9612]","-1.9658<br/>[-2.0035, -1.9613]","-1.9655<br/>[-2.0032, -1.9610]","-1.9658<br/>[-2.0035, -1.9613]","-1.9658<br/>[-2.0035, -1.9613]","-1.9656<br/>[-2.0033, -1.9611]","-1.9656<br/>[-2.0032, -1.9611]","-1.9657<br/>[-2.0034, -1.9612]","-1.9654<br/>[-2.0031, -1.9609]","-1.9656<br/>[-2.0033, -1.9611]","-1.9657<br/>[-2.0034, -1.9612]","-1.9655<br/>[-2.0032, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9656<br/>[-2.0033, -1.9611]","-1.9656<br/>[-2.0033, -1.9611]","-1.9656<br/>[-2.0032, -1.9610]","-1.9656<br/>[-2.0033, -1.9611]","-1.9655<br/>[-2.0032, -1.9610]","-1.9657<br/>[-2.0034, -1.9612]","-1.9657<br/>[-2.0034, -1.9612]","-1.9655<br/>[-2.0031, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9655<br/>[-2.0031, -1.9610]","-1.9655<br/>[-2.0031, -1.9610]","-1.9655<br/>[-2.0031, -1.9610]","-1.9655<br/>[-2.0032, -1.9610]","-1.9654<br/>[-2.0031, -1.9609]"],["-1.4497<br/>[-1.5025, -1.4110]","-1.4783<br/>[-1.5568, -1.4359]","-1.4518<br/>[-1.5222, -1.3952]","-1.5067<br/>[-1.5588, -1.4412]","-1.4894<br/>[-1.5604, -1.4405]","-1.5083<br/>[-1.5671, -1.4459]","-1.5108<br/>[-1.5682, -1.4431]","-1.5505<br/>[-1.6197, -1.4837]","-1.5906<br/>[-1.6597, -1.5089]","-1.5915<br/>[-1.6598, -1.5095]","-1.5151<br/>[-1.5981, -1.4373]","-1.5296<br/>[-1.5975, -1.4554]","-1.5432<br/>[-1.6127, -1.4661]","-1.5430<br/>[-1.6046, -1.4642]","-1.6015<br/>[-1.6871, -1.5419]","-1.5583<br/>[-1.6320, -1.4749]","-1.5444<br/>[-1.6153, -1.4639]","-1.5220<br/>[-1.6213, -1.4545]","-1.6033<br/>[-1.6630, -1.5434]","-1.5555<br/>[-1.6480, -1.4850]","-1.6610<br/>[-1.7451, -1.5953]","-1.5692<br/>[-1.6633, -1.4955]","-1.6192<br/>[-1.7093, -1.5543]","-1.5660<br/>[-1.6425, -1.4733]","-1.5582<br/>[-1.6563, -1.4916]","-1.6908<br/>[-1.7688, -1.6179]","-1.5987<br/>[-1.6941, -1.5277]","-1.5909<br/>[-1.6502, -1.5210]","-1.6143<br/>[-1.6958, -1.5452]","-1.6177<br/>[-1.7212, -1.5314]","-1.6845<br/>[-1.7774, -1.6051]","-1.6189<br/>[-1.7065, -1.5369]","-1.6170<br/>[-1.7038, -1.5461]","-1.6226<br/>[-1.7334, -1.5343]","-1.6375<br/>[-1.7420, -1.5516]","-1.6340<br/>[-1.7153, -1.5559]","-1.6606<br/>[-1.7636, -1.5728]","-1.6372<br/>[-1.7319, -1.5675]","-1.5876<br/>[-1.6857, -1.4863]","-1.6545<br/>[-1.7412, -1.5750]","-1.6466<br/>[-1.7520, -1.5580]","-1.6887<br/>[-1.7852, -1.5998]","-1.7080<br/>[-1.8172, -1.6331]","-1.7572<br/>[-1.8690, -1.6744]"]],"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_Transformed_fibroblasts","Pituitary","Liver","Testis","Artery_Aorta","Lung","Muscle_Skeletal","Artery_Tibial","Kidney_Cortex","Pancreas","Colon_Transverse","Stomach","Prostate","Adipose_Subcutaneous","Heart_Atrial_Appendage","Small_Intestine_Terminal_Ileum","Artery_Coronary","Cells_EBV-transformed_lymphocytes","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Adrenal_Gland","Adipose_Visceral_(Omentum)","Vagina","Brain_Hypothalamus","Spleen","Heart_Left_Ventricle","Uterus","Esophagus_Mucosa","Ovary","Brain_Substantia_nigra","Colon_Sigmoid","Nerve_Tibial","Breast_Mammary_Tissue","Brain_Amygdala","Esophagus_Gastroesophageal_Junction","Thyroid","Brain_Hippocampus","Whole_Blood","Minor_Salivary_Gland","Brain_Spinal_cord_(cervical_c-1)","Brain_Anterior_cingulate_cortex_(BA24)","Skin_Not_Sun_Exposed_(Suprapubic)","Skin_Sun_Exposed_(Lower_leg)","Brain_Cortex","Esophagus_Muscularis","Brain_Cerebellum","Brain_Frontal_Cortex_(BA9)","Brain_Cerebellar_Hemisphere"],[11244,9452,8345,7692,14472,8468,8136,12113,8453,7852,7892,9343,8780,10475,10235,8691,12892,7839,11472,11558,11808,12466,10407,6982,11231,7167,10321,12823,7153,11898,12907,11044,12428,10256,11392,14781,11769,11273,6401,7972,12966,12101,7039,6930,11912,14709,10543,13751,13477],[18.3254024800665,10.7799416439012,8.73311438536271,7.79971794095342,7.62132452338925,7.40724310774107,6.45591385879573,6.20231325525797,6.10520342656813,5.6322068974752,4.77647440625197,4.18999839322467,3.7586864862432,3.65114333283018,3.55290064848093,3.20960137966592,2.95246826188612,2.36614007409046,2.13817865007549,2.10910051986182,2.10553919250995,1.84597029889556,1.60638268073385,1.51436190210134,1.37448347892661,1.35899920609692,0.936502345116312,0.924115716341414,0.696000734349766,0.658098146651879,0.521329381468328,0.51686393949539,0.181686761601315,-0.141142235356972,-0.278460615627348,-0.325846106073278,-0.402031047725978,-0.577700159199306,-0.62390552405103,-0.680095627354523,-0.698009884505788,-0.815602515831223,-0.818523204534655,-0.836013016404087,-0.894576431090626,-0.905778696208704,-0.995007626710223,-1.26898030910312,-1.33647005967644],["-1.9668<br/>[-2.0046, -1.9623]","-1.9662<br/>[-2.0039, -1.9617]","-1.9660<br/>[-2.0037, -1.9615]","-1.9658<br/>[-2.0036, -1.9613]","-1.9663<br/>[-2.0040, -1.9618]","-1.9660<br/>[-2.0037, -1.9615]","-1.9660<br/>[-2.0037, -1.9615]","-1.9661<br/>[-2.0039, -1.9616]","-1.9657<br/>[-2.0034, -1.9612]","-1.9657<br/>[-2.0034, -1.9612]","-1.9656<br/>[-2.0033, -1.9611]","-1.9659<br/>[-2.0036, -1.9614]","-1.9658<br/>[-2.0035, -1.9613]","-1.9655<br/>[-2.0032, -1.9610]","-1.9657<br/>[-2.0034, -1.9612]","-1.9655<br/>[-2.0032, -1.9610]","-1.9660<br/>[-2.0037, -1.9615]","-1.9656<br/>[-2.0033, -1.9611]","-1.9653<br/>[-2.0030, -1.9608]","-1.9653<br/>[-2.0030, -1.9608]","-1.9653<br/>[-2.0030, -1.9608]","-1.9653<br/>[-2.0030, -1.9608]","-1.9655<br/>[-2.0032, -1.9610]","-1.9653<br/>[-2.0030, -1.9608]","-1.9653<br/>[-2.0029, -1.9608]","-1.9654<br/>[-2.0031, -1.9609]","-1.9654<br/>[-2.0031, -1.9609]","-1.9654<br/>[-2.0031, -1.9609]","-1.9654<br/>[-2.0030, -1.9609]","-1.9654<br/>[-2.0031, -1.9609]","-1.9650<br/>[-2.0026, -1.9605]","-1.9654<br/>[-2.0031, -1.9609]","-1.9652<br/>[-2.0029, -1.9607]","-1.9652<br/>[-2.0028, -1.9607]","-1.9653<br/>[-2.0030, -1.9608]","-1.9651<br/>[-2.0028, -1.9606]","-1.9652<br/>[-2.0028, -1.9607]","-1.9653<br/>[-2.0029, -1.9608]","-1.9653<br/>[-2.0030, -1.9608]","-1.9651<br/>[-2.0027, -1.9606]","-1.9653<br/>[-2.0029, -1.9608]","-1.9652<br/>[-2.0029, -1.9607]","-1.9651<br/>[-2.0028, -1.9606]","-1.9651<br/>[-2.0028, -1.9606]","-1.9651<br/>[-2.0028, -1.9606]","-1.9650<br/>[-2.0026, -1.9605]","-1.9651<br/>[-2.0027, -1.9606]","-1.9650<br/>[-2.0026, -1.9605]","-1.9648<br/>[-2.0024, -1.9603]"],["-1.5202<br/>[-1.5245, -1.4991]","-1.6519<br/>[-1.7125, -1.6037]","-1.6773<br/>[-1.7524, -1.6266]","-1.6747<br/>[-1.7396, -1.6154]","-1.7308<br/>[-1.7814, -1.6839]","-1.6234<br/>[-1.6920, -1.5489]","-1.6177<br/>[-1.7255, -1.5488]","-1.6672<br/>[-1.7159, -1.6089]","-1.6195<br/>[-1.6411, -1.5510]","-1.6311<br/>[-1.7414, -1.5748]","-1.6497<br/>[-1.7193, -1.5809]","-1.6160<br/>[-1.7609, -1.5526]","-1.7000<br/>[-1.7661, -1.5117]","-1.7992<br/>[-1.8652, -1.7252]","-1.7221<br/>[-1.7933, -1.6488]","-1.7263<br/>[-1.7742, -1.6676]","-1.7486<br/>[-1.8190, -1.6762]","-1.7020<br/>[-1.8104, -1.6294]","-1.8856<br/>[-1.9464, -1.8138]","-1.8858<br/>[-1.9471, -1.8218]","-1.8844<br/>[-1.9472, -1.8224]","-1.8045<br/>[-1.8634, -1.7459]","-1.7630<br/>[-1.8458, -1.6849]","-1.7946<br/>[-1.9001, -1.7298]","-1.8984<br/>[-1.9747, -1.8267]","-1.7317<br/>[-1.8240, -1.6499]","-1.7877<br/>[-1.8607, -1.7107]","-1.8169<br/>[-1.8889, -1.7401]","-1.7560<br/>[-1.8681, -1.6805]","-1.8198<br/>[-1.9508, -1.7506]","-1.9680<br/>[-2.0116, -1.9127]","-1.8272<br/>[-1.9239, -1.7407]","-1.8137<br/>[-1.8999, -1.7658]","-1.8231<br/>[-1.9085, -1.7480]","-1.8463<br/>[-1.9432, -1.7800]","-1.8572<br/>[-1.9361, -1.7849]","-1.8657<br/>[-1.9303, -1.8081]","-1.8642<br/>[-1.9641, -1.8005]","-1.8395<br/>[-1.9217, -1.7398]","-1.8609<br/>[-1.9398, -1.7744]","-1.8681<br/>[-1.9329, -1.7967]","-1.8850<br/>[-1.9988, -1.8207]","-1.8644<br/>[-1.9552, -1.7770]","-1.8663<br/>[-1.9556, -1.7781]","-1.8965<br/>[-1.9900, -1.8252]","-1.8913<br/>[-1.9789, -1.8245]","-1.9168<br/>[-1.9787, -1.8459]","-1.9288<br/>[-2.0155, -1.8670]","-1.9567<br/>[-2.0044, -1.9153]"]],"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":[["11","5","1","4","13","8","6","9","16","10","19","12","7","3","2","17","18","20","14","15"],[10787,11504,7326,12140,7302,10447,8797,9298,10604,8679,5413,7102,8239,10183,8963,8074,7012,8284,9267,7396],[25.1654085404261,24.8213217355843,19.084401363751,18.663779836813,18.542522604888,18.3653017366178,17.453916599611,14.879063895997,14.866394157512,14.5562618159097,11.9641167542146,11.5876455621886,11.549432076241,11.2822868826447,9.7520259749596,5.78100030318389,5.68494362289316,4.42385293849789,3.50531287495735,1.96820010357393],["-1.9664<br/>[-2.0041, -1.9619]","-1.9671<br/>[-2.0049, -1.9626]","-1.9664<br/>[-2.0042, -1.9619]","-1.9660<br/>[-2.0038, -1.9615]","-1.9663<br/>[-2.0040, -1.9618]","-1.9668<br/>[-2.0045, -1.9623]","-1.9661<br/>[-2.0038, -1.9616]","-1.9666<br/>[-2.0043, -1.9621]","-1.9665<br/>[-2.0043, -1.9620]","-1.9663<br/>[-2.0041, -1.9618]","-1.9662<br/>[-2.0040, -1.9617]","-1.9661<br/>[-2.0038, -1.9616]","-1.9658<br/>[-2.0035, -1.9613]","-1.9661<br/>[-2.0038, -1.9616]","-1.9662<br/>[-2.0039, -1.9617]","-1.9658<br/>[-2.0034, -1.9613]","-1.9658<br/>[-2.0035, -1.9612]","-1.9659<br/>[-2.0036, -1.9614]","-1.9656<br/>[-2.0033, -1.9611]","-1.9655<br/>[-2.0032, -1.9610]"],["-1.6307<br/>[-1.6887, -1.5868]","-1.5251<br/>[-1.5452, -1.4972]","-1.4583<br/>[-1.5315, -1.4224]","-1.6473<br/>[-1.7118, -1.6150]","-1.5520<br/>[-1.6006, -1.5159]","-1.5285<br/>[-1.5320, -1.5134]","-1.5866<br/>[-1.6435, -1.5347]","-1.5359<br/>[-1.5890, -1.5047]","-1.5622<br/>[-1.6353, -1.5157]","-1.5530<br/>[-1.6240, -1.4646]","-1.5172<br/>[-1.5908, -1.4512]","-1.5851<br/>[-1.6398, -1.5342]","-1.6158<br/>[-1.6803, -1.5866]","-1.6331<br/>[-1.6930, -1.5800]","-1.5715<br/>[-1.6457, -1.5191]","-1.6650<br/>[-1.7369, -1.5891]","-1.6123<br/>[-1.6638, -1.5636]","-1.6662<br/>[-1.7479, -1.5966]","-1.7592<br/>[-1.8447, -1.6898]","-1.7135<br/>[-1.8185, -1.6395]"]],"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">devtools<span class="op">::</span><span class="kw">session_info</span>()</a></code></pre></div>
<pre><code>Session info -------------------------------------------------------------</code></pre>
<pre><code> setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-10-05 </code></pre>
<pre><code>Packages -----------------------------------------------------------------</code></pre>
<pre><code> package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.1 2018-07-05 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.5.0)
compiler 3.5.1 2018-07-05 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
crosstalk 1.0.0 2016-12-21 CRAN (R 3.5.0)
datasets * 3.5.1 2018-07-05 local
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.0)
dplyr * 0.7.6 2018-06-29 CRAN (R 3.5.1)
DT * 0.4 2018-01-30 CRAN (R 3.5.0)
evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 CRAN (R 3.5.0)
graphics * 3.5.1 2018-07-05 local
grDevices * 3.5.1 2018-07-05 local
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
htmlwidgets 1.3 2018-09-30 CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
later 0.7.5 2018-09-18 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.1 2018-07-05 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.5.0)
promises 1.0.1 2018-04-13 CRAN (R 3.5.0)
purrr 0.2.5 2018-05-29 CRAN (R 3.5.0)
R.matlab * 3.6.2 2018-09-27 CRAN (R 3.5.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.5.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.5.0)
R.utils 2.7.0 2018-08-27 CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 CRAN (R 3.5.0)
Rcpp 0.12.19 2018-10-01 CRAN (R 3.5.0)
rlang 0.2.2 2018-08-16 CRAN (R 3.5.0)
rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
shiny 1.1.0 2018-05-17 CRAN (R 3.5.0)
stats * 3.5.1 2018-07-05 local
stringi 1.2.4 2018-07-20 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tools 3.5.1 2018-07-05 local
utils * 3.5.1 2018-07-05 local
whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
workflowr 1.1.1 2018-07-06 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)</code></pre>
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