{"id":17931,"date":"2019-12-13T16:39:27","date_gmt":"2019-12-13T15:39:27","guid":{"rendered":"https:\/\/news.embl.de\/?p=17931"},"modified":"2024-03-22T10:50:59","modified_gmt":"2024-03-22T09:50:59","slug":"machine-learning-finds-functional-human-phosphosites","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/","title":{"rendered":"Machine learning finds critical phosphosites"},"content":{"rendered":"\n<p>Researchers at the EMBL\u2019s European Bioinformatics Institute (EMBL-EBI) have created the largest reference phosphoproteome to date of almost 120 000 human phosphosites. To identify those most likely to be critical, they used a machine learning approach capable of ranking them according to functional importance.<\/p>\n\n\n\n<p>Proteins are the core molecular machines of the cell that can be regulated by protein modifications, akin to molecular switches. Protein phosphorylation is one such molecular switch that can cause a protein to become activated, deactivated or modify its function. Despite decades of work number of these modifications critical for life remains a mystery.<\/p>\n\n\n\n<p>This research, <a href=\"https:\/\/www.nature.com\/articles\/s41587-019-0344-3\">published in <em>Nature Biotechnology<\/em><\/a>, creates a freely-accessible resource that can be used by researchers to better understand which proteins are phosphorylated and which phosphosites have functional relevance. Access to this data has significant implications to accelerate the progression of research into many different biological processes and diseases.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Machine learning and data sharing<\/h2>\n\n\n\n<p>\u201cThis new resource would not have been possible if scientists around the world didn\u2019t share their research data and results,\u201d says <a href=\"https:\/\/www.ebi.ac.uk\/research\/beltrao\">Pedro Beltrao, Group Leader at the EMBL-EBI<\/a>. \u201cIt would take a single machine over 500 days to run the mass spectrometry experiments used to create this database. By applying machine learning to this huge dataset, we created a scoring system to help researchers determine which lesser-known phosphosites to explore next.\u201d<\/p>\n\n\n\n<p>The researchers at EMBL-EBI curated over 100 publicly available phospho-enriched human datasets containing over 6000 mass-spectrometry experiments from EMBL-EBI\u2019s <a href=\"https:\/\/www.ebi.ac.uk\/pride\/archive\/\">PRoteomics IDEntifications (PRIDE) database<\/a>. This large-scale project has generated the biggest open access reference phosphoproteome database to date.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Functional human phosphosites<\/h2>\n\n\n\n<p>To identify the most critical phosphosites, researchers used machine learning to integrate diverse annotations for each site such as the degree of conservation. The phosphosite functional score this creates has enormous potential to help other scientists uncover more about their proteins of interest. It can be used to rank known phosphosites to distinguish those which are functionally relevant for molecular processes and disease.<\/p>\n\n\n\n<p>The researchers were able to demonstrate the practicality of their functional score model by identifying two high-scoring phosphosites which play a role in regulating neuronal differentiation.<\/p>\n\n\n\n<p>\u201cThe functional score model created from this study can be used to uncover an abundance of new, functional phosphosites that may play crucial roles in disease,\u201d says David Ochoa, Project Coordinator at <a href=\"https:\/\/www.opentargets.org\/\">Open Targets<\/a>. \u201cWe already know of several groups using the scoring model. We would like to encourage researchers everywhere to explore the resource and make use of it.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Resource has implications for disease research<\/p>\n","protected":false},"author":77,"featured_media":17937,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[28,64,782,36,1748],"embl_taxonomy":[],"class_list":["post-17931","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bioinformatics","tag-cell-biology","tag-database","tag-embl-ebi","tag-press-release"],"acf":{"article_intro":"<p>A new resource for identifying functional human phosphorites relevant for diverse biological processes and disease<\/p>\n","related_links":[{"link_description":"How coding opens up scientific data","link_url":"https:\/\/news.embl.de\/science\/how-coding-opens-up-scientific-data\/"},{"link_description":"Convention on the Rights of the Child stored in DNA","link_url":"https:\/\/news.embl.de\/science\/convention-rights-child-stored-in-dna\/"},{"link_description":"Programming: language","link_url":"https:\/\/news.embl.de\/science\/programming-language\/"}],"article_sources":[{"source_description":"<p>Ochoa, <em>et al. Nature Biotechnology,\u00a0<\/em>(published online) 9 December 2019,\u00a0DOI:10.1038\/s41587-019-0344-3<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1038\/s41587-019-0344-3"}],"vf_locked":false,"featured":false,"color":"#007B53","show_featured_image":false,"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","translations":false,"press_contact":"EMBL-EBI Generic"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Machine learning finds critical phosphosites | EMBL<\/title>\n<meta name=\"description\" content=\"Researchers at EMBL-EBI create a resource for identifying functional human phosphosites relevant for diverse biological processes and disease\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Machine learning finds critical phosphosites | EMBL\" \/>\n<meta property=\"og:description\" content=\"Researchers at EMBL-EBI create a resource for identifying functional human phosphosites relevant for diverse biological processes and disease\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2019-12-13T15:39:27+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T09:50:59+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/12\/Beltrao_Phosphoproteome_620x425.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"425\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Vicky Hatch\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Vicky Hatch\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/\"},\"author\":{\"name\":\"Vicky Hatch\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/d8477ba2d7a6164b141a3872a25ee982\"},\"headline\":\"Machine learning finds critical phosphosites\",\"datePublished\":\"2019-12-13T15:39:27+00:00\",\"dateModified\":\"2024-03-22T09:50:59+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/\"},\"wordCount\":415,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/12\/Beltrao_Phosphoproteome_620x425.jpg\",\"keywords\":[\"bioinformatics\",\"cell biology\",\"database\",\"embl-ebi\",\"press release\"],\"articleSection\":[\"Science\",\"Science &amp; 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Credit: Spencer Phillips\"},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.embl.org\/news\/#website\",\"url\":\"https:\/\/www.embl.org\/news\/\",\"name\":\"European Molecular Biology Laboratory News\",\"description\":\"News from the European Molecular Biology Laboratory\",\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"alternateName\":\"EMBL News\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.embl.org\/news\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/www.embl.org\/news\/#organization\",\"name\":\"European Molecular Biology Laboratory\",\"alternateName\":\"EMBL\",\"url\":\"https:\/\/www.embl.org\/news\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png\",\"width\":300,\"height\":144,\"caption\":\"European Molecular Biology Laboratory\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/embl.org\/\",\"https:\/\/x.com\/embl\",\"https:\/\/www.instagram.com\/embl_org\/\",\"https:\/\/www.linkedin.com\/company\/15813\/\",\"https:\/\/www.youtube.com\/user\/emblmedia\/\"]},{\"@type\":\"Person\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/d8477ba2d7a6164b141a3872a25ee982\",\"name\":\"Vicky Hatch\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/6d864d58088d9e60f42c501aa30714d303efc1ca5aed268210905409910b90d5?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/6d864d58088d9e60f42c501aa30714d303efc1ca5aed268210905409910b90d5?s=96&d=mm&r=g\",\"caption\":\"Vicky Hatch\"},\"url\":\"https:\/\/www.embl.org\/news\/author\/vicky-hatch-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2--2\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Machine learning finds critical phosphosites | EMBL","description":"Researchers at EMBL-EBI create a resource for identifying functional human phosphosites relevant for diverse biological processes and disease","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/","og_locale":"en_US","og_type":"article","og_title":"Machine learning finds critical phosphosites | EMBL","og_description":"Researchers at EMBL-EBI create a resource for identifying functional human phosphosites relevant for diverse biological processes and disease","og_url":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/","og_site_name":"EMBL","article_publisher":"https:\/\/www.facebook.com\/embl.org\/","article_published_time":"2019-12-13T15:39:27+00:00","article_modified_time":"2024-03-22T09:50:59+00:00","og_image":[{"width":620,"height":425,"url":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/12\/Beltrao_Phosphoproteome_620x425.jpg","type":"image\/jpeg"}],"author":"Vicky Hatch","twitter_card":"summary_large_image","twitter_creator":"@embl","twitter_site":"@embl","twitter_misc":{"Written by":"Vicky Hatch","Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"NewsArticle","@id":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/#article","isPartOf":{"@id":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/"},"author":{"name":"Vicky Hatch","@id":"https:\/\/www.embl.org\/news\/#\/schema\/person\/d8477ba2d7a6164b141a3872a25ee982"},"headline":"Machine learning finds critical phosphosites","datePublished":"2019-12-13T15:39:27+00:00","dateModified":"2024-03-22T09:50:59+00:00","mainEntityOfPage":{"@id":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/"},"wordCount":415,"publisher":{"@id":"https:\/\/www.embl.org\/news\/#organization"},"image":{"@id":"https:\/\/www.embl.org\/news\/science\/machine-learning-finds-functional-human-phosphosites\/#primaryimage"},"thumbnailUrl":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2019\/12\/Beltrao_Phosphoproteome_620x425.jpg","keywords":["bioinformatics","cell biology","database","embl-ebi","press release"],"articleSection":["Science","Science &amp; 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