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<h1 class="title toc-ignore">Enrichment results of mean cell haemoglobin concentration</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
</div>
<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/61c4091edf531974a1e5eb618ecf2a3ba0b80e6a" target="_blank">61c4091</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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BioSystems)","Syndecan-3-mediated signaling events<br/>(pid, BioSystems)","Syndecan-3-mediated signaling events<br/>(pid, PC)","Orexin and neuropeptides FF and QRFP bind to their respective receptors<br/>(reactome, PC)","leukotriene biosynthesis<br/>(biocyc, BioSystems)","Regulation of pyruvate dehydrogenase (PDH) complex<br/>(reactome, BioSystems)","B Cell Receptor Complex<br/>(biocarta, BioCarta)","coenzyme A biosynthesis<br/>(humancyc, PC)","Coenzyme A biosynthesis<br/>(reactome, PC)","Carbohydrate digestion and absorption<br/>(kegg, BioSystems)","General transcription regulation<br/>(panther, PANTHER)","General transcription regulation<br/>(panther, PC)","RNA Polymerase III Transcription Initiation From Type 3 Promoter<br/>(reactome, PC)","NrCAM interactions<br/>(reactome, PC)","Arf6 signaling events<br/>(pid, PC)","histidine degradation<br/>(humancyc, PC)","Notch signaling<br/>(kegg, BioSystems)","Histidine catabolism<br/>(reactome, PC)","Arf6 signaling events<br/>(pid, BioSystems)","Glucocorticoid biosynthesis<br/>(reactome, PC)","leukotriene biosynthesis<br/>(humancyc, PC)","Nitrogen metabolism<br/>(kegg, PC)","Synthesis of Leukotrienes (LT) and Eoxins (EX)<br/>(reactome, PC)","O-glycosylation of TSR domain-containing proteins<br/>(reactome, PC)","mRNA splicing<br/>(panther, PC)","Glucagon-type ligand receptors<br/>(reactome, PC)","tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate<br/>(humancyc, PC)","Proteoglycan syndecan-mediated signaling events<br/>(pid, PC)","Attachment of GPI anchor to uPAR<br/>(reactome, PC)","Peptide hormone biosynthesis<br/>(reactome, PC)","RNA polymerase III transcription<br/>(biocarta, BioCarta)","Aldosterone-regulated sodium reabsorption<br/>(kegg, BioSystems)","Synthesis of Lipoxins (LX)<br/>(reactome, PC)","Fibronectin matrix formation<br/>(reactome, PC)","Axonal growth inhibition (RHOA activation)<br/>(reactome, PC)","Melanocyte Development and Pigmentation Pathway<br/>(biocarta, BioCarta)","Vitamin B1 (thiamin) metabolism<br/>(reactome, PC)","Miscellaneous transport and binding events<br/>(reactome, BioSystems)","Metabolism of folate and pterines<br/>(reactome, PC)","Ahr Signal Transduction Pathway<br/>(biocarta, BioCarta)","Mitochondrial iron-sulfur cluster biogenesis<br/>(reactome, PC)","Regulation of lipolysis in adipocytes<br/>(kegg, BioSystems)","Na+-dependent glucose transporters<br/>(reactome, PC)","Spliceosome, Prp19/CDC5L complex<br/>(kegg, BioSystems)","EGFR-dependent Endothelin signaling events<br/>(pid, BioSystems)","EGFR-dependent Endothelin signaling events<br/>(pid, PC)","Synthesis of pyrophosphates in the cytosol<br/>(reactome, PC)","Thyroxine (Thyroid Hormone) Production<br/>(wiki, BioSystems)","Hormone ligand-binding receptors<br/>(reactome, PC)","Mineral absorption<br/>(kegg, BioSystems)","IL 17 Signaling Pathway<br/>(biocarta, BioCarta)","RNA Polymerase I Promoter Opening<br/>(reactome, PC)","Methionine degradation<br/>(kegg, BioSystems)","DNA methylation<br/>(reactome, PC)","Proteasome, 20S core particle<br/>(kegg, BioSystems)","NADH dehydrogenase (ubiquinone) 1 alpha subcomplex<br/>(kegg, BioSystems)","Apoptotic cleavage of cell adhesion proteins<br/>(reactome, PC)","Transport of organic anions<br/>(reactome, PC)","Histidine metabolism<br/>(kegg, PC)","Arachidonic acid metabolism<br/>(kegg, BioSystems)","Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells<br/>(biocarta, BioCarta)","Recycling of bile acids and salts<br/>(reactome, PC)","G0 and Early G1<br/>(reactome, PC)","Synthesis of Leukotrienes (LT) and Eoxins (EX)<br/>(reactome, BioSystems)","Inositol transporters<br/>(reactome, PC)","Histidine metabolism<br/>(kegg, BioSystems)","Vitamin B5 (pantothenate) metabolism<br/>(reactome, PC)","Basigin interactions<br/>(reactome, PC)","Eicosanoid Synthesis<br/>(wiki, BioSystems)","CDK Regulation of DNA Replication<br/>(biocarta, BioCarta)","Arachidonic acid...<br/>(kegg, PC)","Serotonin Transporter Activity<br/>(wiki, BioSystems)","Immunoproteasome<br/>(kegg, BioSystems)","Androgen biosynthesis<br/>(reactome, PC)","Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3<br/>(reactome, BioSystems)","Recycling of bile acids and salts<br/>(reactome, BioSystems)","Signal amplification<br/>(reactome, PC)","p75NTR regulates axonogenesis<br/>(reactome, PC)","Autoimmune thyroid disease<br/>(kegg, BioSystems)","Proximal tubule bicarbonate reclamation<br/>(kegg, BioSystems)","SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription<br/>(reactome, PC)","SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription<br/>(reactome, BioSystems)","Pre-NOTCH Transcription and Translation<br/>(reactome, PC)","Cyclin D associated events in G1<br/>(reactome, PC)","Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer<br/>(reactome, PC)","Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer<br/>(reactome, BioSystems)"],[7,11,29,25,23,25,16,22,4,5,7,63,44,68,2,16,20,8,5,12,2,6,8,44,25,27,27,6,35,5,16,5,34,8,6,10,21,36,4,30,2,4,7,15,7,38,6,6,8,7,4,16,9,4,9,55,6,13,8,9,8,6,10,47,14,59,10,61,15,14,11,11,15,62,15,16,25,24,7,21,11,24,21,12,24,9,17,11,62,15,31,9,49,21,29,30,28,37,40,41],[699,882,1977,1981,2588,1786,2283,1657,463,385,534,1629,4201,1999,202,1497,1816,749,421,1189,97,477,606,3925,2200,2286,1989,1024,3886,512,1192,526,3757,558,478,1132,1780,6889,419,2720,147,506,655,778,557,4191,610,396,586,818,583,1916,733,261,1055,6438,475,983,859,919,762,884,1156,3962,1099,1126,974,1437,1031,1185,1229,1429,1553,4829,1653,1900,1800,1898,704,2093,808,2136,2095,883,2328,833,883,1048,1870,1829,2758,743,2301,1693,2397,2520,2702,2898,3718,3841],[1133.83882503393,1081.71845235484,1074.64147716314,1074.5038275192,1073.92870624897,1028.62067286511,958.597625705685,925.179122051162,791.833477347551,770.962155985789,770.57529785277,700.824882260901,689.626966242072,683.256196408819,668.467389439089,666.579213029451,654.606362760805,629.251202591133,623.521465445743,609.780689323522,593.253796919534,575.992228119995,575.831114572688,560.174984851485,557.086817634278,552.392377548059,546.562230533254,544.051129682564,523.555552770827,498.78479786287,489.227598025738,481.004484832629,463.452983690252,458.070730681517,454.188827313808,453.703052962841,452.988904366742,444.623415786856,418.830804983486,411.764976191391,407.446004161436,389.579153727076,367.477915490694,365.801709587658,363.256211707812,346.314253728835,331.747800020928,315.509491069086,315.152449898764,310.01479277047,307.048586043646,276.515920220582,272.139497198453,246.109790122245,218.951625382293,207.086356113769,202.713644945117,155.245201761127,104.518212223088,104.487266981422,58.7060316780353,30.1787138153126,30.0021634396991,11.6608187915369,5.88781176803119,0.0428505446902053,-0.00101534882537136,-0.0255501144411901,-0.0297619035865747,-0.0337120385675804,-0.0340668471810901,-0.0386305537959007,-0.041187091887661,-0.0435035806682883,-0.0445000808701865,-0.0468470934512509,-0.046864661004247,-0.0504597718565621,-0.0516359648991083,-0.0516819913650482,-0.0527286628408591,-0.0543718690776914,-0.0544109502572812,-0.0598018337437594,-0.0602664535203555,-0.060506082108479,-0.0630959223086514,-0.0709835722655743,-0.0862806879203722,-0.100189410433557,-0.108835696809024,-0.113106707970161,-0.123061667659439,-0.171498963992049,-0.199061687600859,-0.203540225067536,-0.211600776270309,-0.213972090071011,-0.238637420330083,-0.241793357272979],["-5.9172<br/>[-6.2694, -5.6187]","-5.9172<br/>[-6.2694, -5.6187]","-5.9171<br/>[-6.2691, -5.6187]","-5.9171<br/>[-6.2691, -5.6187]","-5.9166<br/>[-6.2687, -5.6181]","-5.9172<br/>[-6.2692, -5.6188]","-5.9167<br/>[-6.2689, -5.6182]","-5.9169<br/>[-6.2691, -5.6184]","-5.9173<br/>[-6.2695, -5.6188]","-5.9174<br/>[-6.2696, -5.6188]","-5.9174<br/>[-6.2695, -5.6189]","-5.9173<br/>[-6.2694, -5.6189]","-5.9160<br/>[-6.2681, -5.6176]","-5.9172<br/>[-6.2692, -5.6188]","-5.9174<br/>[-6.2696, -5.6189]","-5.9170<br/>[-6.2692, -5.6185]","-5.9169<br/>[-6.2690, -5.6184]","-5.9172<br/>[-6.2694, -5.6187]","-5.9173<br/>[-6.2695, -5.6188]","-5.9171<br/>[-6.2693, -5.6186]","-5.9175<br/>[-6.2697, -5.6189]","-5.9173<br/>[-6.2695, -5.6188]","-5.9174<br/>[-6.2695, -5.6189]","-5.9162<br/>[-6.2683, -5.6178]","-5.9167<br/>[-6.2689, -5.6182]","-5.9167<br/>[-6.2689, -5.6182]","-5.9168<br/>[-6.2690, -5.6183]","-5.9175<br/>[-6.2695, -5.6192]","-5.9161<br/>[-6.2683, -5.6177]","-5.9173<br/>[-6.2695, -5.6188]","-5.9171<br/>[-6.2693, 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-5.6197]","-5.9172<br/>[-6.2694, -5.6187]","-5.9167<br/>[-6.2688, -5.6182]","-5.9169<br/>[-6.2691, -5.6184]","-5.9167<br/>[-6.2688, -5.6182]","-5.9166<br/>[-6.2688, -5.6182]","-5.9165<br/>[-6.2687, -5.6181]","-5.9166<br/>[-6.2687, -5.6181]","-5.9162<br/>[-6.2683, -5.6178]","-5.9162<br/>[-6.2683, -5.6178]"],["-1.6374<br/>[-1.6374, -1.6374]","-1.7317<br/>[-1.7317, -1.7317]","-2.5169<br/>[-2.5175, -2.5162]","-2.5178<br/>[-2.5184, -2.5170]","-2.6346<br/>[-2.6347, -2.6345]","-2.4439<br/>[-2.4439, -2.4419]","-2.7373<br/>[-2.7373, -2.7356]","-2.0898<br/>[-2.0898, -2.0897]","-1.3741<br/>[-1.3741, -1.3741]","-2.1081<br/>[-2.1083, -2.1077]","-2.2495<br/>[-2.2503, -2.2487]","-2.1571<br/>[-2.1571, -2.1571]","-3.0276<br/>[-3.0276, -3.0273]","-2.2279<br/>[-2.2280, -2.2279]","-1.6062<br/>[-1.6063, -1.6060]","-2.0841<br/>[-2.0845, -2.0841]","-2.1654<br/>[-2.1654, -2.1651]","-2.5734<br/>[-2.5734, -2.5734]","-2.0218<br/>[-2.0221, -2.0214]","-2.3755<br/>[-2.3760, -2.3747]","-1.3846<br/>[-1.3847, -1.3845]","-2.3771<br/>[-2.3774, -2.3765]","-2.4801<br/>[-2.4813, -2.4783]","-2.8239<br/>[-2.8241, -2.8239]","-2.4648<br/>[-2.4648, -2.4620]","-2.4798<br/>[-2.4798, -2.4768]","-1.9910<br/>[-1.9910, -1.9904]","-1.7437<br/>[-1.7437, -1.7437]","-2.3701<br/>[-2.3701, -2.3701]","-2.1065<br/>[-2.1070, -2.1057]","-2.4737<br/>[-2.4741, -2.4732]","-1.8715<br/>[-1.8716, -1.8715]","-2.4867<br/>[-2.4867, -2.4865]","-1.7942<br/>[-1.8254, -1.7921]","-2.3779<br/>[-2.3784, -2.3771]","-2.7523<br/>[-2.7527, -2.7516]","-2.9490<br/>[-2.9493, -2.9484]","-2.8948<br/>[-2.8948, -2.8926]","-2.3207<br/>[-2.3211, -2.3200]","-2.3246<br/>[-2.3246, -2.3245]","-1.4683<br/>[-1.4683, -1.4682]","-2.2266<br/>[-2.2269, -2.2261]","-2.5146<br/>[-2.5152, -2.5139]","-2.5896<br/>[-2.5899, -2.5890]","-2.4441<br/>[-2.4444, -2.4434]","-2.4806<br/>[-2.4806, -2.4794]","-2.4838<br/>[-2.4843, -2.4831]","-2.2960<br/>[-2.2966, -2.2949]","-2.4663<br/>[-2.4668, -2.4655]","-2.6105<br/>[-2.6116, -2.6085]","-2.2844<br/>[-2.2845, -2.2838]","-2.9811<br/>[-2.9813, -2.9807]","-2.5635<br/>[-2.5641, -2.5628]","-2.1152<br/>[-2.1156, -2.1146]","-2.6950<br/>[-2.6964, -2.6887]","-3.0528<br/>[-3.0528, -3.0480]","-2.3731<br/>[-2.3755, -2.3696]","-2.6883<br/>[-2.6913, -2.6846]","-2.6282<br/>[-2.6328, -2.6225]","-2.6574<br/>[-2.6621, -2.6516]","-2.5706<br/>[-2.5807, -2.5564]","-2.4615<br/>[-2.4686, -2.4505]","-2.5730<br/>[-2.5848, -2.5553]","-2.7020<br/>[-2.7053, -2.6832]","-2.7162<br/>[-2.7399, -2.6800]","-3.6312<br/>[-5.6252, -3.0621]","-6.7964<br/>[-7.8233, -6.2825]","-4.6541<br/>[-6.5342, -4.0872]","-5.6460<br/>[-7.7914, -5.0144]","-5.6380<br/>[-7.7728, -5.0089]","-5.4232<br/>[-7.5497, -4.7934]","-5.3768<br/>[-7.4800, -4.7439]","-5.3189<br/>[-7.4292, -4.6874]","-5.5515<br/>[-7.2464, -4.9608]","-5.4888<br/>[-7.5844, -4.8605]","-5.1432<br/>[-7.1956, -4.5158]","-5.3359<br/>[-7.4304, -4.7045]","-5.5591<br/>[-7.6474, -4.9301]","-5.0663<br/>[-7.5578, -4.4067]","-5.1931<br/>[-7.2759, -4.5645]","-4.6435<br/>[-7.1106, -3.9837]","-5.3671<br/>[-7.4435, -4.7381]","-5.4894<br/>[-7.5675, -4.8627]","-4.8821<br/>[-7.3027, -4.2183]","-5.6413<br/>[-7.7029, -5.0155]","-5.3767<br/>[-7.8471, -4.7155]","-5.3221<br/>[-7.7819, -4.6627]","-5.1726<br/>[-7.6063, -4.5123]","-4.5699<br/>[-6.6187, -3.9703]","-4.9240<br/>[-7.1842, -4.2655]","-4.5790<br/>[-6.5561, -3.9489]","-5.0233<br/>[-7.6941, -4.3304]","-5.3711<br/>[-7.6245, -4.7030]","-5.1857<br/>[-7.5901, -4.5155]","-5.1816<br/>[-7.4753, -4.5109]","-5.2081<br/>[-7.4850, -4.5475]","-5.3895<br/>[-7.6339, -4.7189]","-5.1434<br/>[-7.3712, -4.4665]","-5.3358<br/>[-7.4820, -4.6848]","-5.3530<br/>[-7.4882, -4.6948]"]],"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":[["Pancreas","Brain - Cerebellar Hemisphere","Brain - Cerebellum","Testis","Spleen","Whole Blood","Small Intestine - Terminal Ileum","Cells - EBV-transformed lymphocytes","Lung","Liver","Colon - Transverse","Stomach","Nerve - Tibial","Prostate","Adipose - Subcutaneous","Heart - Left Ventricle","Esophagus - Mucosa","Breast - Mammary Tissue","Muscle - Skeletal","Adrenal Gland","Brain - Hippocampus","Uterus","Heart - Atrial Appendage","Adipose - Visceral (Omentum)","Esophagus - Gastroesophageal Junction","Skin - Sun Exposed (Lower leg)","Vagina","Skin - Not Sun Exposed (Suprapubic)","Brain - Hypothalamus","Brain - Cortex","Colon - Sigmoid","Brain - Anterior cingulate cortex (BA24)","Pituitary","Ovary","Cells - Transformed fibroblasts","Artery - Tibial","Esophagus - Muscularis","Artery - Coronary","Thyroid","Brain - Nucleus accumbens (basal ganglia)","Brain - Frontal Cortex (BA9)","Artery - Aorta","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)"],[5453,6007,6057,6266,4293,6241,4990,5274,5335,6702,5545,5593,6056,5954,5995,5946,5949,5945,6002,6004,6105,6031,6203,6227,6148,6091,6155,6168,6245,6219,6254,6294,6252,6236,6474,6423,6354,6564,6546,6494,6586,6729,6901,6978],[413.059363069832,31.4487975952568,31.4467823764077,31.4177603255718,-0.509021041914179,-0.521507764778595,-0.52250317258339,-0.529237635591399,-0.530216403694185,-0.534085508374963,-0.534256205615255,-0.534726909594971,-0.537144283212979,-0.539015718232738,-0.539908325349556,-0.541231237939194,-0.541235151825131,-0.541418659342559,-0.541425866153855,-0.541649273244583,-0.542926011833399,-0.542926759811792,-0.543527861660863,-0.543966823088422,-0.544127098828066,-0.544197774396936,-0.544864164966942,-0.54543144678289,-0.545457263580346,-0.545851780700185,-0.545946428552588,-0.546027153190807,-0.546347905964466,-0.546679590183147,-0.546789681131875,-0.547107463372893,-0.54748586603282,-0.549421181912927,-0.549430938137014,-0.549732741176555,-0.55041320331027,-0.552159280282717,-0.555993683788129,-0.557054019997972],["-5.9156<br/>[-6.2677, -5.6171]","-5.9170<br/>[-6.2682, -5.6194]","-5.9168<br/>[-6.2681, -5.6191]","-5.9167<br/>[-6.2681, -5.6190]","-5.9160<br/>[-6.2681, -5.6175]","-5.9168<br/>[-6.2682, -5.6189]","-5.9158<br/>[-6.2679, -5.6174]","-5.9156<br/>[-6.2677, -5.6172]","-5.9156<br/>[-6.2677, -5.6172]","-5.9161<br/>[-6.2676, -5.6182]","-5.9155<br/>[-6.2676, -5.6171]","-5.9155<br/>[-6.2676, -5.6171]","-5.9156<br/>[-6.2676, -5.6174]","-5.9155<br/>[-6.2675, -5.6171]","-5.9155<br/>[-6.2675, -5.6171]","-5.9154<br/>[-6.2675, -5.6170]","-5.9154<br/>[-6.2675, -5.6170]","-5.9154<br/>[-6.2675, -5.6170]","-5.9154<br/>[-6.2675, -5.6170]","-5.9154<br/>[-6.2675, -5.6170]","-5.9154<br/>[-6.2674, -5.6170]","-5.9153<br/>[-6.2674, -5.6169]","-5.9154<br/>[-6.2674, -5.6170]","-5.9154<br/>[-6.2674, -5.6170]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6169]","-5.9153<br/>[-6.2674, -5.6168]","-5.9154<br/>[-6.2673, -5.6171]","-5.9153<br/>[-6.2673, -5.6170]","-5.9153<br/>[-6.2673, -5.6169]","-5.9153<br/>[-6.2673, -5.6169]","-5.9153<br/>[-6.2673, -5.6169]","-5.9152<br/>[-6.2673, -5.6168]","-5.9152<br/>[-6.2673, -5.6169]","-5.9152<br/>[-6.2672, -5.6169]","-5.9151<br/>[-6.2671, -5.6167]","-5.9151<br/>[-6.2671, -5.6167]"],["-2.6980<br/>[-2.6980, -2.6975]","-3.4716<br/>[-3.4775, -3.4627]","-3.4778<br/>[-3.4811, -3.4723]","-3.4923<br/>[-3.4959, -3.4865]","-5.5728<br/>[-7.6580, -4.9170]","-4.9565<br/>[-6.6849, -4.3096]","-5.5271<br/>[-7.5663, -4.8817]","-5.6495<br/>[-7.6669, -5.0059]","-5.6377<br/>[-7.6498, -4.9953]","-5.0330<br/>[-6.9739, -4.3837]","-5.6655<br/>[-7.6654, -5.0208]","-5.6334<br/>[-7.6321, -4.9878]","-5.3537<br/>[-7.2979, -4.7103]","-5.5172<br/>[-7.4801, -4.8785]","-5.5316<br/>[-7.4906, -4.8927]","-5.6790<br/>[-7.6573, -5.0376]","-5.6751<br/>[-7.6530, -5.0337]","-5.6974<br/>[-7.6736, -5.0591]","-5.6194<br/>[-7.5940, -4.9782]","-5.6336<br/>[-7.6104, -4.9942]","-5.6080<br/>[-7.5777, -4.9657]","-5.7057<br/>[-7.6775, -5.0641]","-5.5508<br/>[-7.5001, -4.9093]","-5.5548<br/>[-7.5012, -4.9115]","-5.6460<br/>[-7.6092, -5.0035]","-5.7335<br/>[-7.7018, -5.0905]","-5.6986<br/>[-7.6637, -5.0534]","-5.7319<br/>[-7.6962, -5.0878]","-5.6306<br/>[-7.5918, -4.9861]","-5.6950<br/>[-7.6571, -5.0507]","-5.6566<br/>[-7.6143, -5.0087]","-5.6156<br/>[-7.5755, -4.9698]","-5.6924<br/>[-7.6534, -5.0473]","-5.7471<br/>[-7.7066, -5.1071]","-5.5044<br/>[-7.4271, -4.8666]","-5.5613<br/>[-7.4999, -4.9210]","-5.6539<br/>[-7.6065, -5.0123]","-5.5724<br/>[-7.5038, -4.9355]","-5.5910<br/>[-7.5225, -4.9533]","-5.6616<br/>[-7.6099, -5.0220]","-5.6085<br/>[-7.5548, -4.9677]","-5.5903<br/>[-7.5143, -4.9533]","-5.6747<br/>[-7.6034, -5.0371]","-5.6702<br/>[-7.5960, -5.0331]"]],"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":[["Thyroid","Pancreas","Adrenal_Gland","Brain_Cortex","Brain_Frontal_Cortex_(BA9)","Liver","Kidney_Cortex","Testis","Skin_Sun_Exposed_(Lower_leg)","Vagina","Skin_Not_Sun_Exposed_(Suprapubic)","Esophagus_Mucosa","Spleen","Whole_Blood","Colon_Transverse","Cells_EBV-transformed_lymphocytes","Lung","Pituitary","Minor_Salivary_Gland","Muscle_Skeletal","Small_Intestine_Terminal_Ileum","Breast_Mammary_Tissue","Adipose_Visceral_(Omentum)","Adipose_Subcutaneous","Prostate","Stomach","Brain_Cerebellum","Cells_Transformed_fibroblasts","Colon_Sigmoid","Brain_Hippocampus","Heart_Left_Ventricle","Heart_Atrial_Appendage","Brain_Amygdala","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Spinal_cord_(cervical_c-1)","Ovary","Brain_Caudate_(basal_ganglia)","Brain_Putamen_(basal_ganglia)","Brain_Hypothalamus","Brain_Substantia_nigra","Artery_Tibial","Artery_Coronary","Nerve_Tibial","Uterus","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Cerebellar_Hemisphere","Esophagus_Gastroesophageal_Junction","Artery_Aorta","Esophagus_Muscularis"],[12547,8028,12818,12566,14314,8572,9433,8162,7161,7129,7242,7224,7576,7507,7925,8203,8739,10039,8889,9022,9174,10330,10346,10610,9567,9774,11410,11259,11402,11504,11515,11603,11748,11881,13261,12122,12254,12322,12751,13269,13112,12971,13003,13072,13634,14085,14657,14916,14831],[134.862802809764,83.9011327451532,38.0447968957882,17.3832776793007,17.2672911697847,-0.406370320808193,-0.419685283781189,-0.533818940666715,-0.560473574030781,-0.560533778863111,-0.561494608367377,-0.562628590446103,-0.565137779198389,-0.565374690021657,-0.570960049546664,-0.572828821568343,-0.582134243438289,-0.582163638920289,-0.583993915780159,-0.584086492277059,-0.586062622298789,-0.586400699811025,-0.586804068553765,-0.588646528420687,-0.590200096297101,-0.594540500422854,-0.594694194662838,-0.595717157178916,-0.598095480393508,-0.598660686249663,-0.598668284579106,-0.599480205384565,-0.600618228698532,-0.600977592674567,-0.603808834334589,-0.604191090822485,-0.604235690403225,-0.604509203356067,-0.608340024799147,-0.609464125426483,-0.611294730938543,-0.611851777706836,-0.612310048743667,-0.613336637920256,-0.616579636275715,-0.619364849627763,-0.62613652964221,-0.626415051776172,-0.627550519793148],["-5.9136<br/>[-6.2652, -5.6156]","-5.9151<br/>[-6.2669, -5.6170]","-5.9131<br/>[-6.2649, -5.6148]","-5.9132<br/>[-6.2650, -5.6149]","-5.9125<br/>[-6.2644, -5.6143]","-5.9234<br/>[-6.2706, -5.6296]","-5.9247<br/>[-6.2712, -5.6312]","-5.9192<br/>[-6.2693, -5.6222]","-5.9150<br/>[-6.2670, -5.6166]","-5.9149<br/>[-6.2670, -5.6165]","-5.9149<br/>[-6.2670, -5.6166]","-5.9149<br/>[-6.2670, -5.6165]","-5.9149<br/>[-6.2669, -5.6165]","-5.9148<br/>[-6.2669, -5.6165]","-5.9147<br/>[-6.2667, -5.6164]","-5.9147<br/>[-6.2667, -5.6164]","-5.9144<br/>[-6.2664, -5.6160]","-5.9141<br/>[-6.2660, -5.6158]","-5.9143<br/>[-6.2664, -5.6160]","-5.9144<br/>[-6.2664, -5.6161]","-5.9143<br/>[-6.2663, -5.6160]","-5.9139<br/>[-6.2659, -5.6156]","-5.9139<br/>[-6.2658, -5.6156]","-5.9138<br/>[-6.2658, -5.6156]","-5.9142<br/>[-6.2662, -5.6159]","-5.9140<br/>[-6.2660, -5.6157]","-5.9137<br/>[-6.2655, -5.6156]","-5.9136<br/>[-6.2655, -5.6153]","-5.9134<br/>[-6.2654, -5.6151]","-5.9134<br/>[-6.2654, -5.6151]","-5.9134<br/>[-6.2654, -5.6152]","-5.9134<br/>[-6.2654, -5.6151]","-5.9134<br/>[-6.2653, -5.6151]","-5.9134<br/>[-6.2653, -5.6152]","-5.9137<br/>[-6.2651, -5.6159]","-5.9132<br/>[-6.2652, -5.6150]","-5.9133<br/>[-6.2652, -5.6151]","-5.9133<br/>[-6.2651, -5.6151]","-5.9131<br/>[-6.2650, -5.6149]","-5.9132<br/>[-6.2649, -5.6152]","-5.9130<br/>[-6.2649, -5.6149]","-5.9129<br/>[-6.2648, -5.6147]","-5.9129<br/>[-6.2648, -5.6146]","-5.9128<br/>[-6.2648, -5.6145]","-5.9128<br/>[-6.2646, -5.6146]","-5.9127<br/>[-6.2645, -5.6146]","-5.9123<br/>[-6.2642, -5.6140]","-5.9123<br/>[-6.2642, -5.6142]","-5.9122<br/>[-6.2641, -5.6140]"],["-2.4831<br/>[-2.4832, -2.4819]","-2.1666<br/>[-2.1668, -2.1660]","-2.4976<br/>[-2.4990, -2.4975]","-3.7651<br/>[-3.7975, -3.7144]","-3.8240<br/>[-3.8536, -3.7761]","-4.2688<br/>[-6.1684, -3.7155]","-4.2810<br/>[-6.1217, -3.7231]","-4.9226<br/>[-6.3304, -4.3181]","-5.7328<br/>[-7.6486, -5.0968]","-5.7787<br/>[-7.6947, -5.1425]","-5.7223<br/>[-7.6351, -5.0849]","-5.8515<br/>[-7.7623, -5.2145]","-5.6520<br/>[-7.5527, -5.0139]","-5.7372<br/>[-7.6392, -5.1022]","-5.7373<br/>[-7.6206, -5.1045]","-5.6234<br/>[-7.5018, -4.9895]","-5.8078<br/>[-7.6590, -5.1766]","-5.7306<br/>[-7.5123, -5.0984]","-5.8121<br/>[-7.6579, -5.1778]","-5.7047<br/>[-7.5512, -5.0713]","-5.7185<br/>[-7.5590, -5.0854]","-5.8173<br/>[-7.5919, -5.1778]","-5.8354<br/>[-7.6079, -5.1975]","-5.7868<br/>[-7.5461, -5.1418]","-5.6986<br/>[-7.5283, -5.0706]","-5.8377<br/>[-7.6537, -5.2078]","-5.7140<br/>[-7.4348, -5.0893]","-5.8497<br/>[-7.5931, -5.2176]","-5.9306<br/>[-7.6715, -5.3043]","-5.9007<br/>[-7.6387, -5.2740]","-5.8929<br/>[-7.6310, -5.2668]","-5.8939<br/>[-7.6302, -5.2641]","-5.8814<br/>[-7.6138, -5.2493]","-5.8251<br/>[-7.5546, -5.1924]","-5.4837<br/>[-7.1801, -4.8455]","-5.9015<br/>[-7.6247, -5.2650]","-5.8260<br/>[-7.5458, -5.1906]","-5.8068<br/>[-7.5264, -5.1704]","-5.8197<br/>[-7.5295, -5.1809]","-5.6674<br/>[-7.3722, -5.0350]","-5.8216<br/>[-7.5205, -5.1950]","-5.9344<br/>[-7.6351, -5.3092]","-5.9495<br/>[-7.6470, -5.3225]","-5.9869<br/>[-7.6815, -5.3603]","-5.8893<br/>[-7.5759, -5.2619]","-5.8535<br/>[-7.5106, -5.2347]","-6.0114<br/>[-7.6725, -5.3862]","-5.8948<br/>[-7.5568, -5.2709]","-6.0203<br/>[-7.6772, -5.3906]"]],"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":[["18","20","19","8","1","3","2","13","12","15","10","7","17","9","6","14","11","16","5","4"],[7632,8493,6147,10546,7746,10531,9302,7907,7529,8073,8709,8576,8851,9934,9260,9737,10766,10633,11899,12842],[100.637594614447,37.1135715837357,17.3575577530459,14.0764880732183,-0.526666591379962,-0.541387132416351,-0.556394484506615,-0.557288830007481,-0.566133668014091,-0.572673978640596,-0.576531122408584,-0.579344533969311,-0.581015785602237,-0.584098964639921,-0.587038548707318,-0.593863686538605,-0.599301169540974,-0.602015551956925,-0.614203775292188,-0.625441037399079],["-5.9148<br/>[-6.2668, -5.6164]","-5.9166<br/>[-6.2675, -5.6194]","-5.9219<br/>[-6.2711, -5.6254]","-5.9148<br/>[-6.2662, -5.6170]","-5.9181<br/>[-6.2686, -5.6207]","-5.9180<br/>[-6.2676, -5.6219]","-5.9176<br/>[-6.2680, -5.6205]","-5.9156<br/>[-6.2671, -5.6176]","-5.9148<br/>[-6.2669, -5.6164]","-5.9147<br/>[-6.2667, -5.6163]","-5.9147<br/>[-6.2666, -5.6165]","-5.9145<br/>[-6.2665, -5.6162]","-5.9145<br/>[-6.2664, -5.6162]","-5.9148<br/>[-6.2663, -5.6169]","-5.9143<br/>[-6.2663, -5.6160]","-5.9141<br/>[-6.2661, -5.6157]","-5.9141<br/>[-6.2658, -5.6160]","-5.9139<br/>[-6.2658, -5.6157]","-5.9135<br/>[-6.2653, -5.6153]","-5.9130<br/>[-6.2649, -5.6148]"],["-2.2828<br/>[-2.2829, -2.2819]","-2.3916<br/>[-2.3920, -2.3901]","-2.9376<br/>[-2.9379, -2.9365]","-2.0673<br/>[-2.0749, -2.0673]","-4.8544<br/>[-6.4484, -4.2427]","-4.7816<br/>[-6.5756, -4.1747]","-5.0331<br/>[-6.5391, -4.4490]","-5.2257<br/>[-7.0478, -4.6036]","-5.7759<br/>[-7.6756, -5.1458]","-5.7223<br/>[-7.5993, -5.0874]","-5.5066<br/>[-7.3667, -4.8707]","-5.7464<br/>[-7.6049, -5.1157]","-5.6464<br/>[-7.4909, -5.0168]","-5.3275<br/>[-7.1599, -4.6948]","-5.7180<br/>[-7.5539, -5.0908]","-5.8171<br/>[-7.6340, -5.1874]","-5.5414<br/>[-7.3347, -4.9167]","-5.7300<br/>[-7.5096, -5.1058]","-5.7210<br/>[-7.4739, -5.1000]","-5.8709<br/>[-7.5973, -5.2515]"]],"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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