{"id":1946,"date":"2025-09-12T11:29:40","date_gmt":"2025-09-12T09:29:40","guid":{"rendered":"https:\/\/www.gemma-project.eu\/?page_id=1946"},"modified":"2025-09-25T11:15:47","modified_gmt":"2025-09-25T09:15:47","slug":"omics-integration-for-preclinical-gemma-data","status":"publish","type":"page","link":"https:\/\/www.gemma-project.eu\/it\/toolbox\/omics-integration-for-preclinical-gemma-data\/","title":{"rendered":"Omics integration for preclinical GEMMA Data"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"1946\" class=\"elementor elementor-1946\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-cc3ee14 e-flex e-con-boxed e-con e-parent\" data-id=\"cc3ee14\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-e1ed78b elementor-widget elementor-widget-heading\" data-id=\"e1ed78b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">OMICS INTEGRATION FOR PRECLINICAL GEMMA DATA <\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3b9a298 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"3b9a298\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-ec884a7 e-grid e-con-boxed e-con e-parent\" data-id=\"ec884a7\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-cdac75e elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"cdac75e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-cogs\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTOOL TYPE\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tData analysis, Script\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-34f6fb5 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"34f6fb5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-users\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTARGET USERS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tScience &amp; research\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6979d75 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"6979d75\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-hands-helping\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tLEAD PARTNER\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tTampere University, INRAE \t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ebd0beb elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"ebd0beb\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-chart-line\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tCOMPLETENESS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\t100%\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-f1aa745 e-flex e-con-boxed e-con e-parent\" data-id=\"f1aa745\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-5e5f1f3 elementor-widget elementor-widget-text-editor\" data-id=\"5e5f1f3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h4>OMICS INTEGRATION FOR PRECLINICAL GEMMA DATA<\/h4>\n\nWe developed a computational pipeline with accompanying scripts for the multi-omics integration of data from GEMMA&#8217;s preclinical FMT mouse experiments. We apply machine learning to find the most statistically relevant and discriminant features associating with ASD as well as with FMT dietary groups beginning at the individual data type level. The top features are tested with logistic regression to assess their effect sizes and directionality. Multiomics Integration is additionally performed to detect potential interactions between microbiome, genetics and molecular biomarkers using MixOmics and correlation based testing. The pipeline and approach should be applicable for other data types and designs with minimal changes.\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-8e57372 e-flex e-con-boxed e-con e-parent\" data-id=\"8e57372\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-9be527e elementor-widget elementor-widget-n-accordion\" data-id=\"9be527e\" data-element_type=\"widget\" data-e-type=\"widget\" data-settings=\"{&quot;default_state&quot;:&quot;expanded&quot;,&quot;max_items_expended&quot;:&quot;one&quot;,&quot;n_accordion_animation_duration&quot;:{&quot;unit&quot;:&quot;ms&quot;,&quot;size&quot;:400,&quot;sizes&quot;:[]}}\" data-widget_type=\"nested-accordion.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"e-n-accordion\" aria-label=\"Accordion. Open links with Enter or Space, close with Escape, and navigate with Arrow Keys\">\n\t\t\t\t\t\t<details id=\"e-n-accordion-item-1630\" class=\"e-n-accordion-item\" open>\n\t\t\t\t<summary class=\"e-n-accordion-item-title\" data-accordion-index=\"1\" tabindex=\"0\" aria-expanded=\"true\" aria-controls=\"e-n-accordion-item-1630\" >\n\t\t\t\t\t<span class='e-n-accordion-item-title-header'><div class=\"e-n-accordion-item-title-text\"> INSTRUCTIONS <\/div><\/span>\n\t\t\t\t\t\t\t<span class='e-n-accordion-item-title-icon'>\n\t\t\t<span class='e-opened' ><i aria-hidden=\"true\" class=\"fas fa-minus\"><\/i><\/span>\n\t\t\t<span class='e-closed'><i aria-hidden=\"true\" class=\"fas fa-plus\"><\/i><\/span>\n\t\t<\/span>\n\n\t\t\t\t\t\t<\/summary>\n\t\t\t\t<div role=\"region\" aria-labelledby=\"e-n-accordion-item-1630\" class=\"elementor-element elementor-element-4cfc4ab e-con-full e-flex e-con e-child\" data-id=\"4cfc4ab\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-3a1b92c elementor-widget elementor-widget-text-editor\" data-id=\"3a1b92c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>The scripts are used in R, using the RStudio interface as well as linux terminal for Python XGBoost.<\/p><p>Data will be released after publication.<\/p><p>Additional instructions:\u00a0<a href=\"https:\/\/github.com\/jakelin212\/GEMMA_preclinical\/blob\/main\/README.md\" target=\"_blank\" rel=\"noopener\">https:\/\/github.com\/jakelin212\/GEMMA_preclinical\/blob\/main\/README.md<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/details>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-8c67d43 e-flex e-con-boxed e-con e-parent\" data-id=\"8c67d43\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-e6ba40c elementor-widget elementor-widget-heading\" data-id=\"e6ba40c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">CONTACT<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-ad072d9 e-flex e-con-boxed e-con e-parent\" data-id=\"ad072d9\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-1dc3b23 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"1dc3b23\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-7969b4d e-flex e-con-boxed e-con e-parent\" data-id=\"7969b4d\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-398e0ee elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"398e0ee\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/jake.lin@tuni.fi\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Jake Lin <\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/sylvie.rabot@inrae.fr\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Sylvie Rabot<\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>OMICS INTEGRATION FOR PRECLINICAL GEMMA DATA TOOL TYPE Data analysis, Script TARGET USERS Science &amp; research LEAD PARTNER Tampere University, INRAE COMPLETENESS 100% OMICS INTEGRATION FOR PRECLINICAL GEMMA DATA We developed a computational pipeline with accompanying scripts for the multi-omics integration of data from GEMMA&#8217;s preclinical FMT mouse experiments. We apply machine learning to find&hellip;&nbsp;<a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/omics-integration-for-preclinical-gemma-data\/\" rel=\"bookmark\">Leggi tutto &raquo;<span class=\"screen-reader-text\">Omics integration for preclinical GEMMA Data<\/span><\/a><\/p>","protected":false},"author":1,"featured_media":0,"parent":1966,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-pagebuilder-full-width.php","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-1946","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1946","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/comments?post=1946"}],"version-history":[{"count":16,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1946\/revisions"}],"predecessor-version":[{"id":1965,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1946\/revisions\/1965"}],"up":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966"}],"wp:attachment":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/media?parent=1946"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}