{"id":200,"date":"2020-10-27T11:31:11","date_gmt":"2020-10-27T11:31:11","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/?page_id=200"},"modified":"2021-09-28T16:07:17","modified_gmt":"2021-09-28T16:07:17","slug":"when-to-use-reactome","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/when-to-use-reactome\/","title":{"rendered":"When to use Reactome"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Reactome is an extremely useful starting point to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Understand comprehensive molecular details of a pathway based on&nbsp; available literature<\/li><li>Know how various proteins and small molecules interact <em>in vivo<\/em> to achieve biological functions&nbsp;<\/li><li>Learn crosstalk (shared proteins and reactions) between different pathways&nbsp;<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Researchers with experimental data can benefit from the many analysis tools in Reactome. For example, the following types of empirical data can be used:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Qualitative: induced or suppressed genes and proteins<\/li><li>Quantitative: omics data involving expression levels, concentrations or frequencies<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">More information on the analysis tools can be found in the <a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/course\/reactome-tools-analysis-biological-pathways\" target=\"_blank\" rel=\"noreferrer noopener\">Reactome: Tools for analysis of biological pathways<\/a> course.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">&nbsp;When not to use Reactome<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Reactome is not a database of protein-protein interactions but includes tools that can make use of these data. For a dedicated protein-protein interaction database, we recommend using IntAct. You may find our course <a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/intact-quick-tour\/\" target=\"_blank\">IntAct: Quick tour<\/a> useful.<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Reactome pathways can be extended using external resources but Reactome is not intended as a viewer for large interaction networks. If this is your goal, you may wish to use a visualisation tool such as <a href=\"http:\/\/www.cytoscape.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Cytoscape<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Reactome is an extremely useful starting point to: Understand comprehensive molecular details of a pathway based on&nbsp; available literature Know how various proteins and small molecules interact in vivo to achieve biological functions&nbsp; Learn crosstalk (shared proteins and reactions) between different pathways&nbsp; Researchers with experimental data can benefit from the many analysis tools in Reactome&#8230;.<\/p>\n","protected":false},"author":30,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-200","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/pages\/200","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/users\/30"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/comments?post=200"}],"version-history":[{"count":4,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/pages\/200\/revisions"}],"predecessor-version":[{"id":508,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/pages\/200\/revisions\/508"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-exploring-biological-pathways\/wp-json\/wp\/v2\/media?parent=200"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}