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<h1 class="title toc-ignore">Enrichment results of inflammatory bowel disease</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
</div>
<p><strong>Last updated:</strong> 2018-06-27</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/1d289622f08e5d8b484f7a48fd92cc9a597952d3" target="_blank">1d28962</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/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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BioSystems)","Tuberculosis<br/>(kegg, BioSystems)","Interferon gamma signaling<br/>(reactome, PC)","Interferon gamma signaling<br/>(reactome, BioSystems)","Allograft Rejection<br/>(wiki, BioSystems)","Signaling by Interleukins<br/>(reactome, PC)","Cytokines and Inflammatory Response<br/>(biocarta, BioCarta)","Interferon Signaling<br/>(reactome, BioSystems)","PI3K-Akt signaling pathway<br/>(kegg, BioSystems)","Measles<br/>(kegg, BioSystems)","Interferon Signaling<br/>(reactome, PC)","Osteoclast differentiation<br/>(kegg, BioSystems)","IL6-mediated signaling events<br/>(pid, BioSystems)","IFN-gamma pathway<br/>(pid, PC)","Herpes simplex infection<br/>(kegg, BioSystems)","Signaling events mediated by PTP1B<br/>(pid, PC)","IL-3 Signaling Pathway<br/>(wiki, BioSystems)","B Cell Receptor Signaling Pathway<br/>(wiki, BioSystems)","Type II interferon signaling (IFNG)<br/>(wiki, BioSystems)","Interleukin signaling pathway<br/>(panther, PANTHER)","Interleukin signaling pathway<br/>(panther, PC)","IL6-mediated signaling events<br/>(pid, PC)","IFN-gamma pathway<br/>(pid, BioSystems)","TNF signaling pathway<br/>(kegg, BioSystems)","IL22 Soluble Receptor Signaling Pathway <br/>(biocarta, BioCarta)","Cytokine Network<br/>(biocarta, BioCarta)","GMCSF-mediated signaling events<br/>(pid, PC)","IL-6 Signaling Pathway<br/>(wiki, BioSystems)","IL12 signaling mediated by STAT4<br/>(pid, BioSystems)","Prolactin Signaling Pathway<br/>(wiki, BioSystems)","Influenza A<br/>(kegg, BioSystems)","Signaling events mediated by PTP1B<br/>(pid, BioSystems)","activated TAK1 mediates p38 MAPK activation<br/>(reactome, PC)","Leptin signaling pathway<br/>(wiki, BioSystems)","Pathways in cancer<br/>(kegg, BioSystems)","Cytokines and Inflammatory Response<br/>(wiki, BioSystems)","Signaling events mediated by TCPTP<br/>(pid, PC)","IL4-mediated signaling events<br/>(pid, PC)","Interleukin-6 signaling<br/>(reactome, PC)","IL12 signaling mediated by STAT4<br/>(pid, PC)","Dendritic cells in regulating TH1 and TH2 Development<br/>(biocarta, BioCarta)","Calcium signaling in the CD4+ TCR pathway<br/>(pid, PC)","Regulation of IFNG signaling<br/>(reactome, PC)","TRAF6 Mediated Induction of proinflammatory cytokines<br/>(reactome, PC)","Epstein-Barr virus infection<br/>(kegg, BioSystems)","MAP kinase activation in TLR cascade<br/>(reactome, PC)","IL4-mediated signaling events<br/>(pid, BioSystems)","JAK-STAT signaling<br/>(kegg, BioSystems)","Amoebiasis<br/>(kegg, BioSystems)","IL2-mediated signaling events<br/>(pid, BioSystems)","Intestinal immune network for IgA production<br/>(kegg, BioSystems)","Rheumatoid arthritis<br/>(kegg, BioSystems)","Cellular responses to stress<br/>(reactome, BioSystems)","Calcineurin-regulated NFAT-dependent transcription in lymphocytes<br/>(pid, PC)","IL2-mediated signaling events<br/>(pid, PC)","IL 18 Signaling Pathway<br/>(biocarta, BioCarta)","Interferon alpha/beta signaling<br/>(reactome, PC)","Natural killer cell mediated cytotoxicity<br/>(kegg, BioSystems)","Platelet activation, signaling and aggregation<br/>(reactome, BioSystems)","IL-5 Signaling Pathway<br/>(wiki, BioSystems)","MyD88 cascade initiated on plasma membrane<br/>(reactome, PC)","IL-7 Signaling Pathway<br/>(wiki, BioSystems)","TNF signaling<br/>(reactome, BioSystems)","TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation<br/>(reactome, PC)","Adipocytokine signaling pathway<br/>(kegg, BioSystems)","IL3-mediated signaling events<br/>(pid, PC)","Glucocorticoid receptor regulatory network<br/>(pid, PC)","AP-1 transcription factor network<br/>(pid, PC)","Calcineurin-regulated NFAT-dependent transcription in lymphocytes<br/>(pid, BioSystems)","SHP2 signaling<br/>(pid, PC)","Type I diabetes mellitus<br/>(kegg, BioSystems)","African trypanosomiasis<br/>(kegg, BioSystems)","Chagas disease (American trypanosomiasis)<br/>(kegg, BioSystems)","Systemic lupus erythematosus<br/>(kegg, BioSystems)","Inflammation mediated by chemokine and cytokine signaling pathway<br/>(panther, PC)","HIF-1 signaling pathway<br/>(kegg, BioSystems)","Malaria<br/>(kegg, BioSystems)","T cell receptor signaling pathway<br/>(kegg, BioSystems)","Senescence and Autophagy<br/>(wiki, BioSystems)","Inflammation mediated by chemokine and cytokine signaling pathway<br/>(panther, PANTHER)","TGF Beta Signaling Pathway<br/>(wiki, BioSystems)","Selenium Pathway<br/>(wiki, BioSystems)","Downstream signaling in naive CD8+ T cells<br/>(pid, BioSystems)","Downstream signaling in naïve CD8+ T cells<br/>(pid, PC)","Spinal Cord Injury<br/>(wiki, BioSystems)"],[61,37,253,26,148,59,60,111,16,272,18,20,27,250,68,34,171,67,89,35,103,28,192,335,127,166,127,42,43,174,52,98,153,49,77,81,46,40,108,16,20,36,93,28,73,165,50,14,58,385,25,40,58,11,30,21,28,14,70,195,51,56,19,105,51,44,84,366,46,53,6,65,131,217,67,80,43,15,79,67,26,82,69,45,57,41,34,102,126,187,98,48,101,104,166,53,85,48,64,111],[4624,2990,16657,2005,10368,4463,4463,9404,1355,21356,1591,1880,1958,19760,4551,1521,12238,4550,6319,1477,10099,1729,13352,33422,9651,11279,11165,3593,4323,11795,4887,9327,16395,3413,6605,6845,4123,4025,10070,1274,1609,3307,9092,2268,6749,11692,4682,1427,5209,41009,2401,3624,5111,979,2499,1617,2614,1264,6590,14954,4985,4879,1398,11934,5295,2684,6153,26436,4306,5454,517,3366,9085,22897,6341,7553,4064,1008,7477,6437,2179,7287,6457,4222,6558,2559,4211,9722,5132,17464,10079,3929,9512,9324,16683,5544,7560,4807,5243,12304],[24.2422568941743,23.4902417928431,21.3120868752556,19.5348056718298,16.4446303660897,15.1985205860332,15.1985205860332,15.1598556111399,13.8392719330199,13.6740720997039,13.1776603057459,13.1766666035508,12.6441682699143,11.5874583804453,11.2354782626792,11.204820969025,10.9693219118259,10.380799552313,9.90571267107472,9.37527839499308,9.35321600917466,9.04358696369985,9.01339260961562,8.80407995566726,8.75089940014262,8.44016373998846,8.31208827477884,8.24262721722041,8.17854763352179,8.16439006743847,8.08828586503418,7.96765118723216,7.91027267971258,7.84662144164894,7.82309379519037,7.3407864443523,7.3011942354716,7.25326941801313,7.16930724391574,7.10804546896779,7.04943969966499,7.02734555435842,7.00044798893788,6.99898330178394,6.98320570312506,6.98079119383832,6.87837717639872,6.83457309289952,6.71987344468117,6.62954077337099,6.5557140591719,6.54458753001757,6.51080008664113,6.46383317281764,6.43147956253385,6.39706788126815,6.29832550423344,6.24482004463066,6.16866668851741,6.15040388000477,6.11195865036554,6.01417665187259,5.99954345347653,5.97927002356703,5.9595381609589,5.90841924991345,5.90818095872324,5.88528214211352,5.88356944826078,5.75904987599629,5.75202408703798,5.74693068168968,5.74491596390391,5.70224437996231,5.6696437396016,5.66699979481478,5.64857051474297,5.59308766134045,5.51550444880116,5.5090659641391,5.34863747143428,5.03128445199511,4.99287131734552,4.84691434447668,4.45950859612239,4.27314675687789,3.7769240026353,3.77263746761877,3.41284441623809,3.33832017368638,3.26633769665912,3.22739747561461,3.11744227173692,2.92606455225809,2.86329428973351,2.8360994808173,2.52652665989754,2.29106053631088,2.03804482158001,1.90031940798646],["-2.9292<br/>[-2.9404, -2.8644]","-2.9281<br/>[-2.9391, -2.8635]","-2.9314<br/>[-2.9425, -2.8663]","-2.9269<br/>[-2.9380, -2.8625]","-2.9286<br/>[-2.9397, -2.8640]","-2.9272<br/>[-2.9383, -2.8627]","-2.9272<br/>[-2.9383, -2.8627]","-2.9284<br/>[-2.9395, -2.8634]","-2.9256<br/>[-2.9366, -2.8613]","-2.9292<br/>[-2.9403, -2.8641]","-2.9252<br/>[-2.9362, -2.8609]","-2.9260<br/>[-2.9370, -2.8616]","-2.9251<br/>[-2.9361, -2.8608]","-2.9271<br/>[-2.9382, -2.8621]","-2.9261<br/>[-2.9371, -2.8613]","-2.9246<br/>[-2.9356, -2.8599]","-2.9284<br/>[-2.9394, -2.8633]","-2.9257<br/>[-2.9367, -2.8609]","-2.9259<br/>[-2.9369, -2.8611]","-2.9245<br/>[-2.9355, -2.8598]","-2.9266<br/>[-2.9376, -2.8617]","-2.9241<br/>[-2.9351, -2.8595]","-2.9263<br/>[-2.9374, -2.8615]","-2.9271<br/>[-2.9381, -2.8622]","-2.9271<br/>[-2.9382, -2.8622]","-2.9259<br/>[-2.9369, -2.8611]","-2.9264<br/>[-2.9375, -2.8615]","-2.9244<br/>[-2.9354, -2.8598]","-2.9253<br/>[-2.9363, -2.8606]","-2.9266<br/>[-2.9376, -2.8618]","-2.9259<br/>[-2.9369, -2.8611]","-2.9256<br/>[-2.9366, -2.8608]","-2.9278<br/>[-2.9389, -2.8626]","-2.9247<br/>[-2.9357, -2.8600]","-2.9256<br/>[-2.9366, -2.8612]","-2.9256<br/>[-2.9367, -2.8612]","-2.9244<br/>[-2.9354, -2.8598]","-2.9249<br/>[-2.9359, -2.8602]","-2.9251<br/>[-2.9362, -2.8603]","-2.9241<br/>[-2.9351, -2.8595]","-2.9239<br/>[-2.9350, -2.8593]","-2.9243<br/>[-2.9353, -2.8597]","-2.9260<br/>[-2.9371, -2.8612]","-2.9240<br/>[-2.9350, -2.8593]","-2.9250<br/>[-2.9360, -2.8603]","-2.9269<br/>[-2.9379, -2.8620]","-2.9254<br/>[-2.9365, -2.8607]","-2.9236<br/>[-2.9346, -2.8589]","-2.9250<br/>[-2.9360, -2.8603]","-2.9288<br/>[-2.9400, -2.8638]","-2.9240<br/>[-2.9351, -2.8594]","-2.9248<br/>[-2.9359, -2.8601]","-2.9250<br/>[-2.9360, -2.8603]","-2.9240<br/>[-2.9349, -2.8594]","-2.9240<br/>[-2.9350, -2.8593]","-2.9242<br/>[-2.9352, -2.8596]","-2.9233<br/>[-2.9343, -2.8587]","-2.9241<br/>[-2.9351, -2.8595]","-2.9250<br/>[-2.9360, -2.8603]","-2.9262<br/>[-2.9373, -2.8613]","-2.9248<br/>[-2.9358, -2.8602]","-2.9246<br/>[-2.9356, -2.8600]","-2.9243<br/>[-2.9352, -2.8596]","-2.9247<br/>[-2.9358, -2.8600]","-2.9254<br/>[-2.9365, -2.8606]","-2.9236<br/>[-2.9346, -2.8590]","-2.9243<br/>[-2.9353, -2.8596]","-2.9266<br/>[-2.9377, -2.8616]","-2.9239<br/>[-2.9349, -2.8592]","-2.9254<br/>[-2.9365, -2.8605]","-2.9233<br/>[-2.9344, -2.8588]","-2.9239<br/>[-2.9349, -2.8592]","-2.9246<br/>[-2.9357, -2.8599]","-2.9263<br/>[-2.9373, -2.8615]","-2.9252<br/>[-2.9362, -2.8605]","-2.9250<br/>[-2.9361, -2.8603]","-2.9241<br/>[-2.9351, -2.8594]","-2.9233<br/>[-2.9343, -2.8587]","-2.9250<br/>[-2.9360, -2.8603]","-2.9240<br/>[-2.9350, -2.8594]","-2.9233<br/>[-2.9343, -2.8588]","-2.9247<br/>[-2.9357, -2.8599]","-2.9244<br/>[-2.9355, -2.8597]","-2.9239<br/>[-2.9349, -2.8592]","-2.9248<br/>[-2.9358, -2.8601]","-2.9240<br/>[-2.9350, -2.8594]","-2.9246<br/>[-2.9357, -2.8599]","-2.9250<br/>[-2.9360, -2.8602]","-2.9242<br/>[-2.9352, -2.8595]","-2.9260<br/>[-2.9370, -2.8611]","-2.9246<br/>[-2.9356, -2.8599]","-2.9239<br/>[-2.9350, -2.8593]","-2.9244<br/>[-2.9354, -2.8597]","-2.9241<br/>[-2.9352, -2.8595]","-2.9259<br/>[-2.9370, -2.8611]","-2.9242<br/>[-2.9353, -2.8596]","-2.9244<br/>[-2.9354, -2.8596]","-2.9240<br/>[-2.9350, -2.8593]","-2.9240<br/>[-2.9350, -2.8593]","-2.9241<br/>[-2.9351, -2.8594]"],["-1.6401<br/>[-1.7300, -1.5344]","-1.6034<br/>[-1.7004, -1.5311]","-1.9825<br/>[-2.0910, -1.9060]","-1.4785<br/>[-1.5875, -1.3993]","-1.9684<br/>[-2.0690, -1.8796]","-1.7902<br/>[-1.9020, -1.6904]","-1.7902<br/>[-1.9020, -1.6904]","-1.9260<br/>[-2.0452, -1.8448]","-1.4697<br/>[-1.5859, -1.3796]","-2.1302<br/>[-2.2445, -2.0454]","-1.5115<br/>[-1.6412, -1.4277]","-1.5699<br/>[-1.7002, -1.4819]","-1.5597<br/>[-1.6933, -1.4652]","-2.2165<br/>[-2.3213, -2.1532]","-1.8319<br/>[-1.9786, -1.7350]","-1.5010<br/>[-1.6475, -1.4064]","-2.0790<br/>[-2.1765, -1.9814]","-1.8619<br/>[-1.9981, -1.7598]","-1.9554<br/>[-2.0859, -1.8553]","-1.5362<br/>[-1.6826, -1.4307]","-2.0506<br/>[-2.1725, -1.9508]","-1.6105<br/>[-1.7926, -1.5099]","-2.1432<br/>[-2.2370, -2.0466]","-2.3801<br/>[-2.4597, -2.3077]","-2.0712<br/>[-2.1880, -1.9652]","-2.1208<br/>[-2.2305, -2.0265]","-2.1016<br/>[-2.2371, -2.0036]","-1.8511<br/>[-2.0108, -1.7421]","-1.9310<br/>[-2.0799, -1.8242]","-2.1203<br/>[-2.2726, -2.0351]","-1.9421<br/>[-2.0926, -1.8355]","-2.1917<br/>[-2.3239, -2.1229]","-2.2028<br/>[-2.3203, -2.1004]","-1.8619<br/>[-2.0207, -1.7469]","-2.0167<br/>[-2.1538, -1.9113]","-2.0251<br/>[-2.1813, -1.9274]","-1.9169<br/>[-2.0745, -1.8021]","-1.9443<br/>[-2.0899, -1.8289]","-2.2164<br/>[-2.3584, -2.1584]","-1.5783<br/>[-1.7563, -1.4508]","-1.6441<br/>[-1.8473, -1.5372]","-2.0213<br/>[-2.1869, -1.8392]","-2.1094<br/>[-2.2388, -2.0019]","-1.8072<br/>[-1.9846, -1.6832]","-2.0707<br/>[-2.2071, -1.9656]","-2.1596<br/>[-2.2932, -2.0762]","-1.9702<br/>[-2.1272, -1.8580]","-1.5857<br/>[-1.6601, -1.5068]","-2.0062<br/>[-2.1524, -1.8782]","-2.3682<br/>[-2.5249, -2.2789]","-1.8428<br/>[-2.0144, -1.7279]","-1.8644<br/>[-2.0291, -1.7462]","-1.9875<br/>[-2.1352, -1.8629]","-1.5768<br/>[-1.7504, -1.4413]","-1.8564<br/>[-2.0202, -1.7243]","-1.6810<br/>[-1.9145, -1.5556]","-1.8737<br/>[-2.1762, -1.7371]","-1.6514<br/>[-1.8282, -1.5128]","-2.0338<br/>[-2.1783, -1.9184]","-2.2141<br/>[-2.3417, -2.1032]","-1.9664<br/>[-2.1273, -1.8389]","-1.9869<br/>[-2.1488, -1.8624]","-1.6872<br/>[-1.8668, -1.5494]","-2.3046<br/>[-2.4111, -2.2137]","-2.0374<br/>[-2.1885, -1.9220]","-1.8197<br/>[-1.9905, -1.6925]","-2.1986<br/>[-2.3821, -2.1030]","-2.3431<br/>[-2.4752, -2.2423]","-1.9724<br/>[-2.1502, -1.8504]","-2.0523<br/>[-2.2128, -1.9402]","-1.3944<br/>[-1.5504, -1.2202]","-1.9330<br/>[-2.1228, -1.8074]","-2.2712<br/>[-2.3888, -2.1922]","-2.2974<br/>[-2.4357, -2.2024]","-2.0641<br/>[-2.2163, -1.9418]","-2.0753<br/>[-2.2215, -1.9569]","-1.9898<br/>[-2.1522, -1.8699]","-1.6594<br/>[-1.9442, -1.5191]","-2.0815<br/>[-2.2473, -1.9731]","-2.2062<br/>[-2.3860, -2.0915]","-2.0362<br/>[-2.2426, -1.8323]","-2.1149<br/>[-2.2802, -1.9938]","-2.0711<br/>[-2.2508, -1.9537]","-2.0147<br/>[-2.1913, -1.8859]","-2.1192<br/>[-2.3006, -1.9965]","-1.9147<br/>[-2.1098, -1.7692]","-2.0929<br/>[-2.2606, -1.9596]","-2.2023<br/>[-2.3481, -2.0852]","-2.1345<br/>[-2.3341, -2.0044]","-2.3842<br/>[-2.5315, -2.2712]","-2.2586<br/>[-2.3954, -2.1784]","-2.0721<br/>[-2.2901, -1.9275]","-2.2760<br/>[-2.4499, -2.1537]","-2.2669<br/>[-2.4481, -2.1341]","-2.3966<br/>[-2.5368, -2.2760]","-2.1586<br/>[-2.3677, -2.0126]","-2.2581<br/>[-2.4539, -2.1162]","-2.1739<br/>[-2.3952, -2.0253]","-2.2116<br/>[-2.4357, -2.0639]","-2.3698<br/>[-2.5355, -2.2337]"]],"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","Muscle - Skeletal","Brain - Cerebellum","Colon - Transverse","Brain - Cerebellar Hemisphere","Whole Blood","Heart - Atrial Appendage","Artery - Coronary","Pituitary","Adrenal Gland","Stomach","Ovary","Brain - Anterior cingulate cortex (BA24)","Thyroid","Small Intestine - Terminal Ileum","Adipose - Subcutaneous","Adipose - Visceral (Omentum)","Lung","Artery - Tibial","Uterus","Vagina","Esophagus - Muscularis","Brain - Cortex","Breast - Mammary Tissue","Heart - Left Ventricle","Esophagus - Gastroesophageal Junction","Colon - Sigmoid","Prostate","Spleen","Artery - Aorta","Brain - Caudate (basal ganglia)","Nerve - Tibial","Pancreas","Brain - Nucleus accumbens (basal ganglia)","Brain - Frontal Cortex (BA9)","Brain - Hypothalamus","Cells - EBV-transformed lymphocytes","Cells - Transformed fibroblasts","Brain - Hippocampus","Brain - Putamen (basal ganglia)","Skin - Not Sun Exposed (Suprapubic)","Skin - Sun Exposed (Lower leg)","Esophagus - Mucosa","Liver"],[5914,5787,5576,5424,5566,5789,5724,6244,5922,5667,5381,5945,5817,6282,4763,5652,5822,4957,6120,5780,5883,6067,5716,5657,5709,5940,6038,5676,3982,6453,6448,5708,5218,6131,6112,5834,5155,6195,5701,6539,5890,5898,5724,6420],[1.18052158782487,0.711362097559565,0.70915881920922,0.706576183791207,0.650864831036821,0.606956713015112,0.597214363600186,0.522168834179902,0.447700608521483,0.339615262854263,0.332014790682624,0.212318875127591,0.173568338252865,0.155595566257988,0.12145418359094,0.0889483601119853,0.0640817006961324,-0.0238470937800449,-0.0681372099715859,-0.069570230241043,-0.10155498553228,-0.102220269424597,-0.119759652919415,-0.123593953978144,-0.133289037685148,-0.153247886690955,-0.17947824595279,-0.234648212584865,-0.294452751301117,-0.313907269758572,-0.323897028265223,-0.361815963390444,-0.451003014977085,-0.451973275332124,-0.462123450784564,-0.582717440627794,-0.585057094963027,-0.593870154389815,-0.642470705040416,-0.661122739146788,-0.713612136005357,-0.789465820554376,-0.79566177994766,-1.1435371236374],["-2.9235<br/>[-2.9345, -2.8589]","-2.9226<br/>[-2.9336, -2.8582]","-2.9229<br/>[-2.9339, -2.8585]","-2.9233<br/>[-2.9343, -2.8586]","-2.9230<br/>[-2.9340, -2.8585]","-2.9234<br/>[-2.9344, -2.8588]","-2.9222<br/>[-2.9332, -2.8578]","-2.9226<br/>[-2.9336, -2.8581]","-2.9229<br/>[-2.9339, -2.8584]","-2.9226<br/>[-2.9336, -2.8581]","-2.9231<br/>[-2.9341, -2.8585]","-2.9226<br/>[-2.9336, -2.8581]","-2.9230<br/>[-2.9340, -2.8585]","-2.9229<br/>[-2.9339, -2.8584]","-2.9223<br/>[-2.9333, -2.8578]","-2.9226<br/>[-2.9336, -2.8581]","-2.9226<br/>[-2.9336, -2.8581]","-2.9227<br/>[-2.9337, -2.8582]","-2.9228<br/>[-2.9338, -2.8582]","-2.9229<br/>[-2.9339, -2.8583]","-2.9227<br/>[-2.9337, -2.8582]","-2.9227<br/>[-2.9337, -2.8582]","-2.9228<br/>[-2.9338, -2.8582]","-2.9224<br/>[-2.9334, -2.8579]","-2.9223<br/>[-2.9332, -2.8579]","-2.9227<br/>[-2.9337, -2.8581]","-2.9226<br/>[-2.9336, -2.8581]","-2.9227<br/>[-2.9337, -2.8582]","-2.9226<br/>[-2.9336, -2.8581]","-2.9228<br/>[-2.9338, -2.8583]","-2.9226<br/>[-2.9336, -2.8581]","-2.9224<br/>[-2.9334, -2.8579]","-2.9225<br/>[-2.9335, -2.8580]","-2.9225<br/>[-2.9335, -2.8580]","-2.9226<br/>[-2.9336, -2.8581]","-2.9226<br/>[-2.9336, -2.8581]","-2.9225<br/>[-2.9335, -2.8580]","-2.9224<br/>[-2.9334, -2.8580]","-2.9224<br/>[-2.9334, -2.8579]","-2.9222<br/>[-2.9332, -2.8578]","-2.9224<br/>[-2.9333, -2.8579]","-2.9223<br/>[-2.9333, -2.8578]","-2.9222<br/>[-2.9332, -2.8577]","-2.9217<br/>[-2.9327, -2.8573]"],["-2.3013<br/>[-2.5700, -2.1483]","-2.3326<br/>[-2.5967, -2.1510]","-2.3242<br/>[-2.6327, -2.1495]","-2.3394<br/>[-2.6548, -2.1777]","-2.3392<br/>[-2.6140, -2.1545]","-2.3366<br/>[-2.6255, -2.1504]","-2.3708<br/>[-2.6469, -2.2067]","-2.3816<br/>[-2.6612, -2.2092]","-2.3711<br/>[-2.6521, -2.1818]","-2.3819<br/>[-2.7158, -2.2088]","-2.3597<br/>[-2.7197, -2.1782]","-2.3991<br/>[-2.7155, -2.2090]","-2.4158<br/>[-2.7441, -2.2375]","-2.4181<br/>[-2.7349, -2.2353]","-2.4230<br/>[-2.6981, -2.2438]","-2.4217<br/>[-2.7505, -2.2390]","-2.4221<br/>[-2.7594, -2.2368]","-2.4313<br/>[-2.7500, -2.2417]","-2.4579<br/>[-2.7708, -2.2681]","-2.4415<br/>[-2.7572, -2.2370]","-2.4628<br/>[-2.7702, -2.2702]","-2.4651<br/>[-2.7533, -2.2684]","-2.4675<br/>[-2.7531, -2.2701]","-2.4557<br/>[-2.7554, -2.2435]","-2.4776<br/>[-2.7456, -2.2779]","-2.4751<br/>[-2.7560, -2.2726]","-2.4824<br/>[-2.7588, -2.2739]","-2.4779<br/>[-2.7911, -2.2685]","-2.4626<br/>[-2.7798, -2.2452]","-2.5139<br/>[-2.7819, -2.3009]","-2.5231<br/>[-2.7994, -2.3312]","-2.5120<br/>[-2.8017, -2.3010]","-2.5321<br/>[-2.8129, -2.3081]","-2.5583<br/>[-2.8088, -2.3665]","-2.5538<br/>[-2.8592, -2.3602]","-2.5810<br/>[-2.8346, -2.3676]","-2.5771<br/>[-2.8319, -2.3673]","-2.5813<br/>[-2.8415, -2.3634]","-2.5930<br/>[-2.8512, -2.3684]","-2.6106<br/>[-2.8503, -2.3966]","-2.6248<br/>[-2.8560, -2.4025]","-2.6570<br/>[-2.8677, -2.4389]","-2.6650<br/>[-2.8845, -2.4683]","-2.8201<br/>[-2.9711, -2.6171]"]],"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","Lung","Spleen","Whole_Blood","Colon_Transverse","Small_Intestine_Terminal_Ileum","Kidney_Cortex","Minor_Salivary_Gland","Brain_Frontal_Cortex_(BA9)","Cells_EBV-transformed_lymphocytes","Colon_Sigmoid","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Hippocampus","Brain_Caudate_(basal_ganglia)","Adipose_Visceral_(Omentum)","Brain_Cortex","Muscle_Skeletal","Brain_Putamen_(basal_ganglia)","Brain_Amygdala","Stomach","Prostate","Ovary","Pancreas","Nerve_Tibial","Esophagus_Mucosa","Artery_Coronary","Esophagus_Gastroesophageal_Junction","Uterus","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Cerebellum","Vagina","Liver","Pituitary","Brain_Hypothalamus","Esophagus_Muscularis","Artery_Tibial","Cells_Transformed_fibroblasts","Heart_Left_Ventricle","Thyroid","Breast_Mammary_Tissue","Brain_Cerebellar_Hemisphere","Adrenal_Gland","Heart_Atrial_Appendage","Adipose_Subcutaneous","Brain_Substantia_nigra","Artery_Aorta","Brain_Spinal_cord_(cervical_c-1)","Skin_Not_Sun_Exposed_(Suprapubic)","Skin_Sun_Exposed_(Lower_leg)"],[8203,8226,7064,6871,7769,8777,9091,8401,13446,7719,10741,12874,10895,11730,9461,11837,8727,11780,11131,9329,9290,11491,7764,12414,6947,12245,14000,12172,11304,10727,6860,8480,9470,12054,14176,12633,10939,11062,12157,9787,13394,12535,11078,9892,12561,14270,12465,6870,6778],[3.22234663701264,2.30107346758643,1.84763547057344,1.07664920212839,0.914753032111477,0.084238485534543,-0.109660107702603,-0.226443272453151,-0.269571850757079,-0.280450346924138,-0.297371988938741,-0.396679094964794,-0.402873913669616,-0.471383746841018,-0.47437021820141,-0.55451637475088,-0.636199617839322,-0.698397032924846,-0.76762068533725,-0.767675444618065,-0.792598464976536,-0.797185731790443,-0.816330686000309,-0.863392527644905,-0.905627930970389,-0.914529799168932,-0.921776616640583,-0.940621795697514,-0.956789157684149,-0.958734608424411,-0.988093319946879,-0.994364627316457,-0.994473658352435,-1.00887907736365,-1.01206459789561,-1.01255929099626,-1.06084223222589,-1.08397006552489,-1.10347795260857,-1.11540966678585,-1.13969414768336,-1.14512945333877,-1.15060683267761,-1.24374614340724,-1.29104532710121,-1.31059151413052,-1.40142700870611,-2.15636438763395,-2.22890173239518],["-2.9238<br/>[-2.9349, -2.8596]","-2.9227<br/>[-2.9337, -2.8583]","-2.9235<br/>[-2.9345, -2.8589]","-2.9236<br/>[-2.9346, -2.8590]","-2.9233<br/>[-2.9344, -2.8587]","-2.9231<br/>[-2.9341, -2.8585]","-2.9232<br/>[-2.9342, -2.8586]","-2.9228<br/>[-2.9339, -2.8583]","-2.9229<br/>[-2.9339, -2.8583]","-2.9227<br/>[-2.9337, -2.8582]","-2.9234<br/>[-2.9344, -2.8588]","-2.9227<br/>[-2.9338, -2.8582]","-2.9225<br/>[-2.9335, -2.8580]","-2.9221<br/>[-2.9331, -2.8576]","-2.9228<br/>[-2.9338, -2.8583]","-2.9224<br/>[-2.9334, -2.8579]","-2.9221<br/>[-2.9331, -2.8576]","-2.9218<br/>[-2.9328, -2.8574]","-2.9222<br/>[-2.9332, -2.8577]","-2.9225<br/>[-2.9335, -2.8580]","-2.9220<br/>[-2.9330, -2.8576]","-2.9222<br/>[-2.9332, -2.8578]","-2.9233<br/>[-2.9343, -2.8587]","-2.9220<br/>[-2.9330, -2.8577]","-2.9223<br/>[-2.9333, -2.8578]","-2.9218<br/>[-2.9328, -2.8574]","-2.9228<br/>[-2.9338, -2.8582]","-2.9225<br/>[-2.9335, -2.8580]","-2.9221<br/>[-2.9330, -2.8575]","-2.9219<br/>[-2.9329, -2.8575]","-2.9222<br/>[-2.9332, -2.8577]","-2.9220<br/>[-2.9330, -2.8576]","-2.9223<br/>[-2.9333, -2.8578]","-2.9218<br/>[-2.9328, -2.8574]","-2.9225<br/>[-2.9335, -2.8580]","-2.9221<br/>[-2.9331, -2.8577]","-2.9223<br/>[-2.9333, -2.8578]","-2.9218<br/>[-2.9328, -2.8574]","-2.9223<br/>[-2.9333, -2.8578]","-2.9220<br/>[-2.9330, -2.8576]","-2.9217<br/>[-2.9327, -2.8573]","-2.9222<br/>[-2.9332, -2.8577]","-2.9217<br/>[-2.9327, -2.8573]","-2.9215<br/>[-2.9325, -2.8571]","-2.9217<br/>[-2.9327, -2.8573]","-2.9217<br/>[-2.9327, -2.8573]","-2.9213<br/>[-2.9323, -2.8570]","-2.9223<br/>[-2.9333, -2.8578]","-2.9222<br/>[-2.9332, -2.8578]"],["-2.2355<br/>[-2.3743, -2.1170]","-2.3974<br/>[-2.5096, -2.2515]","-2.2799<br/>[-2.4717, -2.1242]","-2.3314<br/>[-2.5890, -2.1752]","-2.3866<br/>[-2.6186, -2.2370]","-2.4872<br/>[-2.7543, -2.3231]","-2.5266<br/>[-2.7927, -2.3543]","-2.5249<br/>[-2.8002, -2.3503]","-2.5999<br/>[-2.8124, -2.4633]","-2.5171<br/>[-2.8087, -2.3236]","-2.5719<br/>[-2.8111, -2.4103]","-2.6204<br/>[-2.8179, -2.4747]","-2.6029<br/>[-2.8177, -2.4439]","-2.6268<br/>[-2.8240, -2.4767]","-2.5903<br/>[-2.8284, -2.4140]","-2.6407<br/>[-2.8323, -2.4790]","-2.6352<br/>[-2.8369, -2.4551]","-2.6739<br/>[-2.8448, -2.5136]","-2.6893<br/>[-2.8522, -2.5401]","-2.6697<br/>[-2.8602, -2.4846]","-2.6749<br/>[-2.8652, -2.4852]","-2.6886<br/>[-2.8624, -2.5128]","-2.4957<br/>[-2.7846, -2.3213]","-2.7095<br/>[-2.8691, -2.5420]","-2.7187<br/>[-2.8768, -2.5401]","-2.7273<br/>[-2.8726, -2.5728]","-2.7260<br/>[-2.9018, -2.5676]","-2.7255<br/>[-2.8860, -2.5430]","-2.7383<br/>[-2.8829, -2.5778]","-2.7372<br/>[-2.9079, -2.5780]","-2.7408<br/>[-2.9112, -2.5376]","-2.7411<br/>[-2.9309, -2.5557]","-2.7459<br/>[-2.8956, -2.5601]","-2.7570<br/>[-2.8899, -2.6066]","-2.7499<br/>[-2.8933, -2.5742]","-2.7526<br/>[-2.8931, -2.5805]","-2.7664<br/>[-2.9075, -2.5846]","-2.7735<br/>[-2.9131, -2.5867]","-2.7837<br/>[-2.9083, -2.6169]","-2.7906<br/>[-2.9497, -2.6236]","-2.7963<br/>[-2.9112, -2.6439]","-2.8006<br/>[-2.9135, -2.6503]","-2.8003<br/>[-2.9256, -2.6222]","-2.8466<br/>[-2.9626, -2.6705]","-2.8542<br/>[-2.9596, -2.6915]","-2.8563<br/>[-2.9775, -2.7180]","-2.9110<br/>[-3.0280, -2.7745]","-2.6719<br/>[-2.8572, -2.4677]","-2.6684<br/>[-2.8549, -2.4717]"]],"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","17","16","13","2","12","5","10","6","9","7","11","3","19","4","14","20","15","8","18"],[7414,8155,9991,7791,8910,7193,11380,8474,8929,9771,8534,10446,10132,5807,12311,9429,8103,7752,10380,7463],[15.7497376956849,3.68821597571714,2.444971723171,2.18838337786028,1.80072244739588,1.70609745394705,1.31329447957526,1.19552693616041,1.16759441765724,0.0348480333135494,-0.122894658265834,-0.163530953700427,-0.193358166474827,-0.226076900856387,-0.290958703903941,-0.513815692104727,-0.595636909361394,-0.629090028375703,-0.641183844071228,-0.650622623140238],["-2.9241<br/>[-2.9351, -2.8594]","-2.9251<br/>[-2.9361, -2.8602]","-2.9233<br/>[-2.9343, -2.8587]","-2.9239<br/>[-2.9349, -2.8593]","-2.9244<br/>[-2.9354, -2.8597]","-2.9234<br/>[-2.9344, -2.8588]","-2.9239<br/>[-2.9349, -2.8593]","-2.9235<br/>[-2.9346, -2.8589]","-2.9232<br/>[-2.9342, -2.8586]","-2.9228<br/>[-2.9338, -2.8583]","-2.9226<br/>[-2.9336, -2.8582]","-2.9219<br/>[-2.9329, -2.8576]","-2.9225<br/>[-2.9335, -2.8580]","-2.9228<br/>[-2.9338, -2.8582]","-2.9232<br/>[-2.9342, -2.8586]","-2.9224<br/>[-2.9334, -2.8579]","-2.9219<br/>[-2.9329, -2.8575]","-2.9223<br/>[-2.9333, -2.8578]","-2.9221<br/>[-2.9331, -2.8577]","-2.9219<br/>[-2.9329, -2.8575]"],["-2.1037<br/>[-2.1335, -2.0548]","-2.2160<br/>[-2.3904, -2.0814]","-2.2921<br/>[-2.4995, -2.1525]","-2.2867<br/>[-2.4936, -2.1415]","-2.2820<br/>[-2.4698, -2.1522]","-2.2745<br/>[-2.5055, -2.1042]","-2.4146<br/>[-2.6113, -2.2583]","-2.3594<br/>[-2.6287, -2.1821]","-2.3767<br/>[-2.6314, -2.2169]","-2.5502<br/>[-2.8048, -2.3782]","-2.5777<br/>[-2.8069, -2.4041]","-2.5915<br/>[-2.8229, -2.4162]","-2.6197<br/>[-2.8123, -2.4838]","-2.5658<br/>[-2.8129, -2.3624]","-2.5144<br/>[-2.7934, -2.3613]","-2.6780<br/>[-2.8545, -2.4983]","-2.6930<br/>[-2.8748, -2.4956]","-2.7064<br/>[-2.8785, -2.5113]","-2.7142<br/>[-2.8780, -2.5305]","-2.7068<br/>[-2.8941, -2.4994]"]],"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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