This information is over 2 years old. Information was current at time of publication.{"id":3965,"date":"2020-11-20T10:11:17","date_gmt":"2020-11-20T15:11:17","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=3965"},"modified":"2020-12-11T10:52:22","modified_gmt":"2020-12-11T15:52:22","slug":"12-9-wksp-geo-pathway-enrichment-analysis","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/11\/20\/12-9-wksp-geo-pathway-enrichment-analysis\/","title":{"rendered":"12\/9 wksp: GEO &amp; Pathway Enrichment Analysis"},"content":{"rendered":"<ul>\n<li><strong><span style=\"color: #19657f\">WHAT:<\/span> <\/strong>GEO Data Mining &amp; Pathway Enrichment Analysis w\/ Open Access Tools<\/li>\n<li><strong><span style=\"color: #19657f\">WHEN:<\/span> <\/strong>December 9th, 10am-12pm &amp; 1-4pm<\/li>\n<li><strong><span style=\"color: #19657f\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #19657f\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #19657f\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/geo-data-mining-pathway-enrichment-analysis-w-open-access-tools\/3720\">here<\/a><\/li>\n<\/ul>\n<p><!--more--><br \/>\n<strong><span style=\"color: #19657f\">Workshop Objective:<\/span><\/strong><\/p>\n<p>This is a 5 hour workshop. The morning session (<strong>10 am &#8211; 12 pm<\/strong>) teaches how to retrieve a list of differentially expressed genes (DEG) associated with a gene expression study by searching GEO using <a href=\"https:\/\/biojupies.cloud\/analyze\">BioJupies <\/a>(RNA-Seq), <a href=\"http:\/\/www.ilincs.org\/apps\/grein\/?gse=\">GREIN<\/a> (RNA-Seq) and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/geo2r\/\">Geo2R <\/a>(Microarray).<\/p>\n<p>The afternoon session (<strong>1 pm &#8211; 4 pm<\/strong>) focuses on uncovering the biology hidden behind the extracted DEG list by searching publicly available pathway enrichment analysis resources including <a href=\"http:\/\/geneontology.org\/\">Gene Ontology (GO),<\/a> <a href=\"http:\/\/software.broadinstitute.org\/gsea\/msigdb\/index.jsp\">Molecular Signature Database (MsigDB)<\/a>, <a href=\"https:\/\/reactome.org\/\">Reactome<\/a>, <a href=\"http:\/\/pantherdb.org\/\">Panther<\/a>, <a href=\"https:\/\/www.genome.jp\/kegg\/pathway.html\">KEGG<\/a>, <a href=\"https:\/\/www.pathwaycommons.org\/\">PathwayCommons<\/a>, and <a href=\"https:\/\/www.wikipathways.org\/index.php\/WikiPathways\">WikiPathways<\/a> using <a href=\"http:\/\/software.broadinstitute.org\/gsea\/index.jsp\">GSEA <\/a>and <a href=\"https:\/\/biit.cs.ut.ee\/gprofiler\/gost\">g:Profiler<\/a>.<\/p>\n<p>One week after the workshop, a follow up session (<strong>1 pm &#8211; 3 pm<\/strong>) will review the hands-on exercise questions distributed during the workshop.\u00a0 We will not be addressing questions on data analysis for personal research projects\u2014researchers are encouraged to\u00a0<a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">request a one-on-one consultation with MBIS<\/a>\u00a0for this type of discussion. Registration is not required for the hands-on follow up session.\u00a0 To attend, use the same Zoom link you receive upon registration for this workshop.<\/p>\n<p><strong><span style=\"color: #19657f\">Target Audience:<\/span><\/strong><\/p>\n<p>Experimental biologists seeking to analyze gene lists generated through omics experiments. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.<\/p>\n<p><strong><span style=\"color: #19657f\">Workshop Guide:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/hsls.libguides.com\/MolBioWorkshops\/pathways\/OATools\">https:\/\/hsls.libguides.com\/MolBioWorkshops\/pathways\/OATools<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #19657f\">Suggested Reading:<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867418307098?via%3Dihub\">Pulikkan, J. A., Hegde, M., Ahmad, H. M., Belaghzal, H., Illendula, A., Yu, J., \u2026 Castilla, L. H. (2018). CBF\u03b2-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. <em>Cell<\/em>, <em>174<\/em>(1), 172\u2013186.e21. doi:10.1016\/j.cell.2018.05.048<\/a><\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41596-018-0103-9\">Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., \u2026 Bader, G. D. (2019). Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols, 14(2), 482\u2013517. doi:10.1038\/s41596-018-0103-9<\/a><\/li>\n<\/ul>\n<p><strong><span style=\"color: #19657f\">Attribution:<\/span><\/strong><\/p>\n<p>Please include the following statement in the acknowledgments section for all publications, posters, and presentations: <strong>Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.<\/strong><\/p>\n<p><a href=\"http:\/\/files.hsls.pitt.edu\/files\/molbio\/MolbioWorkshops.pdf\">HSLS Fall 2020 MolBio Info Service Training Workshops schedule<\/a><\/p>\n<p><a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">Contact<\/a> the <a href=\"http:\/\/www.hsls.pitt.edu\/molbio\">HSLS Molecular Biology Information Service<\/a> with any questions.<\/p>\n<p>(Photo by <a href=\"https:\/\/unsplash.com\/@bracht?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Fabio Bracht<\/a> on <a href=\"https:\/\/unsplash.com\/s\/photos\/pathway-connection?utm_source=unsplash&amp;utm_medium=referral&amp;utm_content=creditCopyText\">Unsplash<\/a>)<\/p>\n","protected":false},"excerpt":{"rendered":"<ul>\n<li><strong><span style=\"color: #19657f\">WHAT:<\/span> <\/strong>GEO Data Mining &amp; Pathway Enrichment Analysis w\/ Open Access Tools<\/li>\n<li><strong><span style=\"color: #19657f\">WHEN:<\/span> <\/strong>December 9th, 10am-12pm &amp; 1-4pm<\/li>\n<li><strong><span style=\"color: #19657f\">WHERE:<\/span> <\/strong>Online; instructions upon registration<\/li>\n<li><strong><span style=\"color: #19657f\">WHO:<\/span> <\/strong>Ansuman Chattopahyay &amp; Sri Chaparala<\/li>\n<li><strong><span style=\"color: #19657f\">HOW:<\/span> <\/strong>Register <a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/geo-data-mining-pathway-enrichment-analysis-w-open-access-tools\/3720\">here<\/a><\/li>\n<\/ul>\n<p><a class=\"read-more\" alt= \"12\/9 wksp: GEO &amp; Pathway Enrichment Analysis\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2020\/11\/20\/12-9-wksp-geo-pathway-enrichment-analysis\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":3635,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-3965","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3965","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/31"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=3965"}],"version-history":[{"count":1,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3965\/revisions"}],"predecessor-version":[{"id":3966,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/3965\/revisions\/3966"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/3635"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=3965"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=3965"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=3965"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}