{"id":100,"date":"2020-04-28T10:55:24","date_gmt":"2020-04-28T10:55:24","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/submitting-data-to-resource-name\/"},"modified":"2021-01-21T15:10:38","modified_gmt":"2021-01-21T15:10:38","slug":"pathway-enrichment-analysis","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/pathway-enrichment-analysis\/","title":{"rendered":"Pathway Enrichment Analysis"},"content":{"rendered":"\n

This analysis is a common approach that provides mechanistic insight into gene lists from high-throughput experiments. Let\u2019s try to perform a pathway enrichment analysis with an example dataset. <\/p>\n\n\n\n

Try it yourself<\/h3>\n\n\n\n

Click on Analyze Tool in the homepage<\/a> to start the analysis. In the pop-up window, there are multiple tabs on the left for different operations. For our case, we need the first tab named Analyse gene list (selected by default). We can select an example file from the list on the right. Let\u2019s click on Tissue Specific Expression (HPA) to load the data in the panel. Notice the data format – first column is protein names and subsequent columns are expression values. Note also that the first column header should start with a # symbol. Next, click on Continue to go to the next screen and Analyse! to start the analysis (Figure 13).<\/p>\n\n\n\n

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Figure 13<\/strong> Pathway enrichment analysis interface in Reactome.<\/figcaption><\/figure><\/div>\n\n\n\n

Soon we will be able to see results of our analysis in various formats – left panel as hierarchically ordered pathways, lower panel as lists and center panel as graphical networks (Figure 14).  Explore the different panels to see how they work!<\/p>\n\n\n\n

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Figure 14<\/strong> Analysis results in pathway browser.<\/figcaption><\/figure><\/div>\n\n\n\n

An interesting visual is the Voronoi map on the top of the graphical panel (Figure 15). Click on this to get a better overview of analysis results.<\/p>\n\n\n\n

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Figure 15<\/strong> Voronoi map (Reacfoam) view of analysis results.<\/figcaption><\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"

This analysis is a common approach that provides mechanistic insight into gene lists from high-throughput experiments. Let\u2019s try to perform a pathway enrichment analysis with an example dataset.  Try it yourself Click on Analyze Tool in the homepage to start the analysis. In the pop-up window, there are multiple tabs on the left for different…<\/p>\n","protected":false},"author":30,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-100","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/pages\/100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/users\/30"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/comments?post=100"}],"version-history":[{"count":10,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/pages\/100\/revisions"}],"predecessor-version":[{"id":342,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/pages\/100\/revisions\/342"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/reactome-quick-tour\/wp-json\/wp\/v2\/media?parent=100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}