{"id":1582,"date":"2017-05-04T10:14:09","date_gmt":"2017-05-04T01:14:09","guid":{"rendered":"http:\/\/www.monomorphic.org\/wordpress\/?p=1582"},"modified":"2017-05-04T10:14:09","modified_gmt":"2017-05-04T01:14:09","slug":"interactive-toxicogenomics","status":"publish","type":"post","link":"https:\/\/www.monomorphic.org\/wordpress\/interactive-toxicogenomics\/","title":{"rendered":"Interactive toxicogenomics"},"content":{"rendered":"<p>If you work in toxicology or drug discovery, you might be familiar with the database <a href=\"http:\/\/toxico.nibiohn.go.jp\/\">Open TG-GATEs<\/a>, a large transcriptomics database that catalogues gene expression response to well-known drugs and toxins. This database was developed by Japan&#8217;s Toxicogenomics Project during many years, as a private-public sector partnership, and remains a very valuable resource. As with many large datasets, despite the open-ness, accessing and working with this data can require considerable work. Data must always be placed in a context, and these contexts must be continually renewed. One user-friendly interface to simplify access to\u00c2\u00a0this data is <a href=\"http:\/\/toxygates.nibiohn.go.jp\">Toxygates<\/a>, which I begun developing as a postdoc at <a href=\"http:\/\/www.nibiohn.go.jp\">NIBIOHN<\/a> in the <a href=\"http:\/\/mizuguchilab.org\/\">Mizuguchi Lab<\/a> in 2012 (and am still the lead developer of). As a web application, Toxygates lets you look at data of interest in context, together with annotations such as gene ontology\u00c2\u00a0terms and metabolic pathways, as well as\u00c2\u00a0visualisation tools.<\/p>\n<p>We are\u00c2\u00a0now releasing a new major version of Toxygates, which, among many other new features, allows you to perform and visualise gene set clustering analyses directly in the web browser. Gene sets can also be easily characterised through an enrichment function, which is supported by the <a href=\"http:\/\/targetmine.mizuguchilab.org\/\">TargetMine<\/a> data warehouse. Last but not least, users can now upload their own data and cluster and analyse it in context, together with the Open TG-GATEs data.<\/p>\n<p>Our\u00c2\u00a0<a href=\"https:\/\/www.nature.com\/articles\/s41598-017-01500-1\">new paper<\/a> in Scientific Reports documents the new version of Toxygates and illustrates the use of the new functions through a case study performed on the hepatotoxic drug WY-14643. If you are curious, <a href=\"http:\/\/toxygates.nibiohn.go.jp\">give it a try<\/a>.<\/p>\n<p>When I begun the development as a quick prototype, I had no idea that the project would still be evolving many years later. Toxygates represents considerable work and many learning experiences for me as a researcher\u00c2\u00a0and software engineer, and I&#8217;m very grateful to everybody who has collaborated with us, supported the project,\u00c2\u00a0and made our\u00c2\u00a0journey possible.<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>If you work in toxicology or drug discovery, you might be familiar with the database Open TG-GATEs, a large transcriptomics database that catalogues gene expression response to well-known drugs and toxins. This database was developed by Japan&#8217;s Toxicogenomics Project during many years, as a private-public sector partnership, and remains a very valuable resource. As with [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[109],"tags":[41,175,176,10,174,177],"class_list":["post-1582","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","tag-academic","tag-omics","tag-open-tggates","tag-research","tag-toxicology","tag-toxygates"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/py2qT-pw","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/posts\/1582","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/comments?post=1582"}],"version-history":[{"count":6,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/posts\/1582\/revisions"}],"predecessor-version":[{"id":1627,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/posts\/1582\/revisions\/1627"}],"wp:attachment":[{"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/media?parent=1582"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/categories?post=1582"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.monomorphic.org\/wordpress\/wp-json\/wp\/v2\/tags?post=1582"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}