{"id":2786,"date":"2023-06-13T01:08:23","date_gmt":"2023-06-13T00:08:23","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&#038;p=2786"},"modified":"2023-06-14T18:37:24","modified_gmt":"2023-06-14T17:37:24","slug":"online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/","title":{"rendered":"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST"},"content":{"rendered":"\n<p>Klaudia Adamowicz<sup>1*<\/sup>, Andreas Maier<sup>1<\/sup>, Jan Baumbach<sup>1,2<\/sup> and David B. Blumenthal<sup>3<\/sup><\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>1<\/sup>Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>2<\/sup>Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>3<\/sup>Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU), Erlangen, Germany<\/p>\n\n\n\n<p>klaudia.adamowicz [at] uni-hamburg.de<\/p>\n\n\n\n<p><strong>Abstract<\/strong><\/p>\n\n\n\n<p class=\"abstract-para\">Given the constraints faced in the development of new drugs, the importance of drug repurposing has reached unprecedented levels. A key aspect of effective drug repurposing lies in the discovery of disease mechanisms and the identification of clusters of diseases with shared mechanistic characteristics. While various methods exist for computing candidate disease mechanisms and clusters, the absence of ground truth presents challenges in validating these predictions through <em>in silico<\/em> means. This obstacle significantly impedes the widespread adoption of <em>in silico<\/em> prediction tools, as experimentalists often hesitate to conduct wet-lab validations without clearly quantified initial plausibility. <\/p>\n\n\n\n<p class=\"abstract-para\">To address this issue, we introduce DIGEST (<em>in silico<\/em> validation of disease and gene sets, clusterings or subnetworks). DIGEST is a Python-based validation tool that offers multiple avenues for utilization. It is accessible as a web interface through <a href=\"https:\/\/digest-validation.net\">https:\/\/digest-validation.net<\/a>, as a stand-alone package, or via a REST API. DIGEST streamlines the process of <em>in silico<\/em> validation by providing fully automated pipelines. These pipelines encompass critical components such as disease and gene ID mapping, enrichment analysis, comparisons of shared genes and variants, and background distribution estimation. Additionally, DIGEST incorporates functionality to automatically update the external databases utilized by the pipelines. By employing DIGEST, users gain the ability to assess the statistical significance of candidate mechanisms in terms of functional and genetic coherence. The tool enables the computation of empirical P-values with ease, requiring only a few simple clicks. With its comprehensive and user-friendly features, DIGEST greatly facilitates the evaluation of candidate mechanisms, empowering researchers to quantify the plausibility of predicted mechanisms in a robust and efficient manner.<\/p>\n\n\n\n<p class=\"abstract-para\"><strong>Keywords:<\/strong> Systems medicine, in silico validation, Functional and genetic coherence<\/p>\n\n\n\n<p class=\"abstract-para\"><strong>Acknowledgement:<\/strong> This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreements No. 777111 (A.M., J.B.). This publication reflects only the authors\u2019 view and the European Commission is not responsible for any use that may be made of the information it contains. This work was supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant 01ZX1908A and grant 01ZX1910D) (J.B.). J.B. was partially funded by his VILLUM Young Investigator Grant No. 13154.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Klaudia Adamowicz<sup>1*<\/sup>, Andreas Maier<sup>1<\/sup>, Jan Baumbach<sup>1,2<\/sup> and David B. Blumenthal<sup>3<\/sup><\/p>\n<p class=\"affiliation-para\"><sup>1<\/sup>Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany<\/p>\n<p class=\"affiliation-para\"><sup>2<\/sup>Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark<\/p>\n<p class=\"affiliation-para\"><sup>3<\/sup>Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU), Erlangen, Germany<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[18],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.0 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Klaudia Adamowicz1*, Andreas Maier1, Jan Baumbach1,2 and David B. Blumenthal31Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany2Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark3Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU), Erlangen, Germany Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-14T17:37:24+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/\",\"name\":\"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST - BelBi 2023\",\"isPartOf\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\"},\"datePublished\":\"2023-06-13T00:08:23+00:00\",\"dateModified\":\"2023-06-14T17:37:24+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/online-in-silico-validation-of-disease-and-gene-sets-clusterings-or-subnetworks-with-digest\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"name\":\"BelBi 2023\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\",\"name\":\"Belgrade Bioinformatics Conference\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"contentUrl\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"width\":278,\"height\":500,\"caption\":\"Belgrade Bioinformatics Conference\"},\"image\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST - BelBi 2023","robots":{"index":"noindex","follow":"follow"},"og_locale":"en_US","og_type":"article","og_title":"Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST - BelBi 2023","og_description":"Klaudia Adamowicz1*, Andreas Maier1, Jan Baumbach1,2 and David B. 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