<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> <meta name="author" content="Joyce Hsiao" /> <title>Expression profile of the gold-standard samples</title> <script src="site_libs/jquery-1.11.3/jquery.min.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> <script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script> <link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" /> <script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script> <link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" /> <script src="site_libs/highlightjs-9.12.0/highlight.js"></script> <link href="site_libs/font-awesome-4.5.0/css/font-awesome.min.css" rel="stylesheet" /> <style type="text/css">code{white-space: pre;}</style> <style type="text/css"> pre:not([class]) { background-color: white; } </style> <script type="text/javascript"> if (window.hljs) { hljs.configure({languages: []}); hljs.initHighlightingOnLoad(); if (document.readyState && document.readyState === "complete") { window.setTimeout(function() { hljs.initHighlighting(); }, 0); } } </script> <style type="text/css"> h1 { font-size: 34px; } h1.title { font-size: 38px; } h2 { font-size: 30px; } h3 { font-size: 24px; } h4 { font-size: 18px; } h5 { font-size: 16px; } h6 { font-size: 12px; } .table th:not([align]) { text-align: left; } </style> </head> <body> <style type = "text/css"> .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } button.code-folding-btn:focus { outline: none; } </style> <style type="text/css"> /* padding for bootstrap navbar */ body { padding-top: 51px; padding-bottom: 40px; } /* offset scroll position for anchor links (for fixed navbar) */ .section h1 { padding-top: 56px; margin-top: -56px; } .section h2 { padding-top: 56px; margin-top: -56px; } .section h3 { padding-top: 56px; margin-top: -56px; } .section h4 { padding-top: 56px; margin-top: -56px; } .section h5 { padding-top: 56px; margin-top: -56px; } .section h6 { padding-top: 56px; margin-top: -56px; } </style> <script> // manage active state of menu based on current page $(document).ready(function () { // active menu anchor href = window.location.pathname href = href.substr(href.lastIndexOf('/') + 1) if (href === "") href = "index.html"; var menuAnchor = $('a[href="' + href + '"]'); // mark it active menuAnchor.parent().addClass('active'); // if it's got a parent navbar menu mark it active as well menuAnchor.closest('li.dropdown').addClass('active'); }); </script> <div class="container-fluid main-container"> <!-- tabsets --> <script> $(document).ready(function () { window.buildTabsets("TOC"); }); </script> <!-- code folding --> <script> $(document).ready(function () { // move toc-ignore selectors from section div to header $('div.section.toc-ignore') .removeClass('toc-ignore') .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); // establish options var options = { selectors: "h1,h2,h3", theme: "bootstrap3", context: '.toc-content', hashGenerator: function (text) { return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); }, ignoreSelector: ".toc-ignore", scrollTo: 0 }; options.showAndHide = true; options.smoothScroll = true; // tocify var toc = $("#TOC").tocify(options).data("toc-tocify"); }); </script> <style type="text/css"> #TOC { margin: 25px 0px 20px 0px; } @media (max-width: 768px) { #TOC { position: relative; width: 100%; } } .toc-content { padding-left: 30px; padding-right: 40px; } div.main-container { max-width: 1200px; } div.tocify { width: 20%; max-width: 260px; max-height: 85%; } @media (min-width: 768px) and (max-width: 991px) { div.tocify { width: 25%; } } @media (max-width: 767px) { div.tocify { width: 100%; max-width: none; } } .tocify ul, .tocify li { line-height: 20px; } .tocify-subheader .tocify-item { font-size: 0.90em; padding-left: 25px; text-indent: 0; } .tocify .list-group-item { border-radius: 0px; } </style> <!-- setup 3col/9col grid for toc_float and main content --> <div class="row-fluid"> <div class="col-xs-12 col-sm-4 col-md-3"> <div id="TOC" class="tocify"> </div> </div> <div class="toc-content col-xs-12 col-sm-8 col-md-9"> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="index.html">fucci-seq</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html">Home</a> </li> <li> <a href="about.html">About</a> </li> <li> <a href="license.html">License</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jdblischak/fucci-seq"> <span class="fa fa-github"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> <!-- Add a small amount of space between sections. --> <style type="text/css"> div.section { padding-top: 12px; } </style> <div class="fluid-row" id="header"> <h1 class="title toc-ignore">Expression profile of the gold-standard samples</h1> <h4 class="author"><em>Joyce Hsiao</em></h4> </div> <!-- The file analysis/chunks.R contains chunks that define default settings shared across the workflowr files. --> <!-- Update knitr chunk options --> <!-- Insert the date the file was last updated --> <p><strong>Last updated:</strong> 2018-02-01</p> <!-- Insert the code version (Git commit SHA1) if Git repository exists and R package git2r is installed --> <p><strong>Code version:</strong> 0f846a1</p> <hr /> <div id="background" class="section level2"> <h2>Background</h2> <p>Here’s the list for which a given gene symbol corresponds to multiple Ensembl gene ID in the data.</p> <p>I learned that there are some regions on the genome that show substantial variability in the population, and subsequently can have multiple representations (sequences). These regions are known as “alternate loci”.</p> <p>I got some of these info from this paper <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155401/" class="uri">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155401/</a>. According to this paper, the GRCh38 patch assembly has a total of 178 alternate-locus-containing regions associated with a total of 261 alternate loci.</p> <p>For example, TAF9 has two alternative loci which correspond to two different Ensembl ID, and you can see the location fo these two here on this page <a href="http://useast.ensembl.org/Homo_sapiens/Gene/Alleles?db=core;g=ENSG00000273841;r=5:69364743-69370013" class="uri">http://useast.ensembl.org/Homo_sapiens/Gene/Alleles?db=core;g=ENSG00000273841;r=5:69364743-69370013</a>. Click on “View alleles of this gene on alternate assemblies”.</p> <p>Another example is TUBB which corresponds to 8 Ensembl IDs. It is located in MHC region which is known to have 8 alternative loci (corresponding to 8 different cell lines; <a href="https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC" class="uri">https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC</a>). So there’s no surprise that TUBB has 8 Ensembl ID.</p> <hr /> </div> <div id="data-and-packages" class="section level2"> <h2>Data and packages</h2> <p>load cell cycle genes from the dropseq paper</p> <pre class="r"><code>cellcycle <- readRDS("../data/cellcycle-genes-previous-studies/rds/macosko-2017.rds") dup <- which(duplicated(cellcycle[,-3])) cellcycle[cellcycle$hgnc %in% unique(cellcycle$hgnc[dup]),]</code></pre> <pre><code> hgnc phase ensembl 81 CCDC84 S ENSG00000280975 82 CCDC84 S ENSG00000186166 114 CDK7 M/G1 ENSG00000134058 115 CDK7 M/G1 ENSG00000277273 132 CFD G2 ENSG00000197766 133 CFD G2 ENSG00000274619 219 FAM189B M/G1 ENSG00000262666 220 FAM189B M/G1 ENSG00000160767 224 FAN1 G2 ENSG00000198690 225 FAN1 G2 ENSG00000276787 231 FOPNL M/G1 ENSG00000276914 232 FOPNL M/G1 ENSG00000133393 289 HRAS G1/S ENSG00000276536 290 HRAS G1/S ENSG00000174775 315 KIAA1147 G1/S ENSG00000257093 316 KIAA1147 G1/S ENSG00000262599 335 KIFC1 G2 ENSG00000204197 336 KIFC1 G2 ENSG00000237649 337 KIFC1 G2 ENSG00000056678 338 KIFC1 G2 ENSG00000233450 373 MDC1 M ENSG00000228575 374 MDC1 M ENSG00000137337 375 MDC1 M ENSG00000225589 376 MDC1 M ENSG00000206481 377 MDC1 M ENSG00000224587 378 MDC1 M ENSG00000234012 379 MDC1 M ENSG00000231135 380 MDC1 M ENSG00000237095 397 MRPS18B M/G1 ENSG00000223775 398 MRPS18B M/G1 ENSG00000226111 399 MRPS18B M/G1 ENSG00000229861 400 MRPS18B M/G1 ENSG00000204568 401 MRPS18B M/G1 ENSG00000203624 402 MRPS18B M/G1 ENSG00000233813 403 MRPS18B M/G1 ENSG00000227420 484 PPP1R10 M ENSG00000238104 485 PPP1R10 M ENSG00000227804 486 PPP1R10 M ENSG00000204569 487 PPP1R10 M ENSG00000230995 488 PPP1R10 M ENSG00000235291 489 PPP1R10 M ENSG00000206489 490 PPP1R10 M ENSG00000231737 558 SMARCB1 M ENSG00000099956 559 SMARCB1 M ENSG00000275837 583 TAF15 G1/S ENSG00000276833 584 TAF15 G1/S ENSG00000270647 585 TAF9 M/G1 ENSG00000273841 586 TAF9 M/G1 ENSG00000276463 624 TUBB G2 ENSG00000232421 625 TUBB G2 ENSG00000224156 626 TUBB G2 ENSG00000235067 627 TUBB G2 ENSG00000183311 628 TUBB G2 ENSG00000229684 629 TUBB G2 ENSG00000227739 630 TUBB G2 ENSG00000196230 631 TUBB G2 ENSG00000232575 646 UBR7 G1/S ENSG00000012963 647 UBR7 G1/S ENSG00000278787</code></pre> <hr /> </div> <div id="session-information" class="section level2"> <h2>Session information</h2> <pre><code>R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Scientific Linux 7.4 (Nitrogen) Matrix products: default BLAS: /home/joycehsiao/miniconda3/envs/fucci-seq/lib/R/lib/libRblas.so LAPACK: /home/joycehsiao/miniconda3/envs/fucci-seq/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.1 backports_1.0.5 magrittr_1.5 rprojroot_1.2 [5] tools_3.4.1 htmltools_0.3.6 yaml_2.1.16 Rcpp_0.12.14 [9] stringi_1.1.2 rmarkdown_1.8 knitr_1.17 git2r_0.19.0 [13] stringr_1.2.0 digest_0.6.12 evaluate_0.10.1</code></pre> </div> <!-- Adjust MathJax settings so that all math formulae are shown using TeX fonts only; see http://docs.mathjax.org/en/latest/configuration.html. This will make the presentation more consistent at the cost of the webpage sometimes taking slightly longer to load. Note that this only works because the footer is added to webpages before the MathJax javascript. --> <script type="text/x-mathjax-config"> MathJax.Hub.Config({ "HTML-CSS": { availableFonts: ["TeX"] } }); </script> <hr> <p> This <a href="http://rmarkdown.rstudio.com">R Markdown</a> site was created with <a href="https://github.com/jdblischak/workflowr">workflowr</a> </p> <hr> <!-- To enable disqus, uncomment the section below and provide your disqus_shortname --> <!-- disqus <div id="disqus_thread"></div> <script type="text/javascript"> /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */ var disqus_shortname = 'rmarkdown'; // required: replace example with your forum shortname /* * * DON'T EDIT BELOW THIS LINE * * */ (function() { var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true; dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js'; (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq); })(); </script> <noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript> <a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a> --> </div> </div> </div> <script> // add bootstrap table styles to pandoc tables function bootstrapStylePandocTables() { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); } $(document).ready(function () { bootstrapStylePandocTables(); }); </script> <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); </script> </body> </html>