{"id":2025,"date":"2025-09-25T11:07:22","date_gmt":"2025-09-25T09:07:22","guid":{"rendered":"https:\/\/www.gemma-project.eu\/?page_id=2025"},"modified":"2025-12-18T09:12:01","modified_gmt":"2025-12-18T08:12:01","slug":"network-based-multi-omics-integration-to-prioritize-features-in-gemma-omics-datasets","status":"publish","type":"page","link":"https:\/\/www.gemma-project.eu\/it\/toolbox\/network-based-multi-omics-integration-to-prioritize-features-in-gemma-omics-datasets\/","title":{"rendered":"NETWORK-BASED MULTI-OMICS INTEGRATION to prioritize features in GEMMA omics DATAsets"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"2025\" class=\"elementor elementor-2025\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-69a1138c e-flex e-con-boxed e-con e-parent\" data-id=\"69a1138c\" 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-78e9a8f9 elementor-widget elementor-widget-heading\" data-id=\"78e9a8f9\" 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\">NETWORK-BASED MULTI-OMICS INTEGRATION TO PRIORITIZE FEATURES IN GEMMA OMICS DATASETS<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-2c015275 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"2c015275\" 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-583ef744 e-grid e-con-boxed e-con e-parent\" data-id=\"583ef744\" 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-46f505c3 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"46f505c3\" 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-2f00a1f7 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"2f00a1f7\" 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-5b9fc7c2 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"5b9fc7c2\" 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\tCNR-ITB\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-1ce5181 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"1ce5181\" 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-332b4603 e-flex e-con-boxed e-con e-parent\" data-id=\"332b4603\" 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-7d284caf elementor-widget elementor-widget-text-editor\" data-id=\"7d284caf\" 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>NETWORK-BASED MULTI-OMICS INTEGRATION TO PRIORITIZE FEATURES IN GEMMA OMICS DATASETS<\/h4>\n<p>We developed a pipeline for the integrative analysis of gene-related, metabolite-related and microbiota species-related data. The pipeline relies on a network of molecular interactions and functional interactions (interactome), and on the network analysis tool \u201cmND\u201d (multi-layer Network Diffusion) [doi: 10.1093\/bioinformatics\/btz652].<\/p>\n<p>Gene-related, metabolite-related and microbiota species-related input scores from GEMMA omics are mapped on the interactome (see \u201cA network of molecular and functional interactions for GEMMA multi-omics data analysis\u201d), and mND is used to prioritize features (genes, metabolites and microbial species), based on their input scores and reciprocal network proximity. The output feature-level score is statistically assessed based on two distinct null models, which test the relation between output scores and input scores, and between output scores and feature-feature interactions.<\/p>\n<p>The top scoring features are selected based on feature-level score, network topology scores (e.g. modularity, connected components), and joint analysis of the two (e.g. distribution of feature score over the network).<\/p>\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-11bb47d5 e-flex e-con-boxed e-con e-parent\" data-id=\"11bb47d5\" 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-77a9395d elementor-widget elementor-widget-n-accordion\" data-id=\"77a9395d\" 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-2000\" 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-2000\" >\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-2000\" class=\"elementor-element elementor-element-43edcbdf e-con-full e-flex e-con e-child\" data-id=\"43edcbdf\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-7acbfe3e elementor-widget elementor-widget-text-editor\" data-id=\"7acbfe3e\" 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 pipeline is written in R and uses BiocParallel\u00a0<\/p><p>[10.18129\/B9.bioc.BiocParallel ] for parallel computations.<\/p><p>Network analysis tool mND:\u00a0<a href=\"https:\/\/github.com\/emosca-cnr\/mND\" target=\"_blank\" rel=\"noopener\">https:\/\/github.com\/emosca-cnr\/mND<\/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-2b6274ae e-flex e-con-boxed e-con e-parent\" data-id=\"2b6274ae\" 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-4a48ff65 elementor-widget elementor-widget-heading\" data-id=\"4a48ff65\" 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-74f85f39 e-flex e-con-boxed e-con e-parent\" data-id=\"74f85f39\" 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-22bbfc0f elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"22bbfc0f\" 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-582ec64d e-flex e-con-boxed e-con e-parent\" data-id=\"582ec64d\" 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-19515160 elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"19515160\" 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:\/\/ettore.mosca@itb.cnr.it\">\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\">Ettore Mosca<\/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>\n\t\t","protected":false},"excerpt":{"rendered":"<p>NETWORK-BASED MULTI-OMICS INTEGRATION TO PRIORITIZE FEATURES IN GEMMA OMICS DATASETS TOOL TYPE Data analysis, Script TARGET USERS Science &amp; research LEAD PARTNER CNR-ITB COMPLETENESS 100% NETWORK-BASED MULTI-OMICS INTEGRATION TO PRIORITIZE FEATURES IN GEMMA OMICS DATASETS We developed a pipeline for the integrative analysis of gene-related, metabolite-related and microbiota species-related data. The pipeline relies on a&hellip;&nbsp;<a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/network-based-multi-omics-integration-to-prioritize-features-in-gemma-omics-datasets\/\" rel=\"bookmark\">Leggi tutto &raquo;<span class=\"screen-reader-text\">NETWORK-BASED MULTI-OMICS INTEGRATION to prioritize features in GEMMA omics DATAsets<\/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-2025","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2025","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=2025"}],"version-history":[{"count":10,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2025\/revisions"}],"predecessor-version":[{"id":2105,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2025\/revisions\/2105"}],"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=2025"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}