The transcription category provides six gene-set libraries that attempt to link differentially expressed genes with the transcriptional machinery. These six libraries include the ability to identify transcription factors that are enriched for target genes within the input list using four different options: 1) ChEA [10]; 2) position weight matrices (PWMs) from TRANSFAC [11] and JASPAR [12]; 3) target genes generated from PMWs downloaded from the UCSC genome browser [13]; and 4) transcription factor targets extracted from the ENCODE project [14, 15]. In addition, the two other gene-set libraries in the transcription category are gene sets associated with: 5) histone modifications extracted from the Roadmap Epigenomics Project [16]; and 6) microRNAs targets computationally predicted by TargetScan [17].
Twogether (1994): Download AVI
Transcription factor target genes inferred from PWMs for the human genome were downloaded from the UCSC Genome Browser [13] FTP site which contains many resources for gene and sequence annotations. We converted this file into a gene set library and included it in Enrichr since it produces different results compared with the other method to identify transcription factor/target interactions from PWMs as described above.
Enrichr has two parts: a back end and a front end. The back end is comprised of a Microsoft IIS 6 web server and Apache Tomcat 7 as the Java application server. The back end uses Java servlets to respond to the submissions of gene lists or for processing other data requests from the front end. Apache Maven is used to compile, minify, and aggregate the JavaScript and CSS files for faster web load times, package, and deploy the web app onto the Tomcat server. Conversely, the front end is written primarily in HTML, CSS, JavaScript, and JSP. Enrichr has a user friendly and responsive interface, using AJAX calls to serve JSON response data from the servlet asynchronously for a smoother user experience. The bar graphs, grids, term networks, and color pickers are dynamically generated using the SVG JavaScript library, D3 [52]. The page transitions, sortable tables, hovering over text functions, touch gestures, and other page manipulations are powered by the jQuery JavaScript library. A shared servlet that is used in other projects is used to convert URL-encoded base64 text that represents the SVG figures into downloadable SVG, PNG, or JPG files using the Batik SVG Toolkit from the Apache XML Graphics Project. Enrichr can also be accessed via Android, iOS, and BlackBerry phone apps. All of the phone apps share the mobile framework, Apache Cordova, which allows for the development of cross-platform mobile apps using HTML5, JavaScript, and CSS ensuring that there is no feature decay across the different mobile platforms as well as desktop web platforms. Slight adjustments in Java, Objective C, and JavaScript for Android, iOS, and BlackBerry respectively were necessary to ensure that Enrichr was functional and consistent across these platforms.
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