{"id":352,"date":"2021-04-05T07:45:19","date_gmt":"2021-04-05T07:45:19","guid":{"rendered":"https:\/\/vinuni.edu.vn\/research\/?p=352"},"modified":"2022-09-05T07:46:24","modified_gmt":"2022-09-05T07:46:24","slug":"improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data","status":"publish","type":"post","link":"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/","title":{"rendered":"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data"},"content":{"rendered":"<p>Abstract<\/p>\n<p>The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. In this study, we presented an improved driver gene identification and analysis pipeline that comprises the four most widely focused analyses for driver genes: enrichment analysis, clinical feature association with expression profiles of identified driver genes as well as with their functional modules, and patient stratification by existing advanced computational tools integrating multi-omics data. The improved pipeline\u2019s general usability was demonstrated straightforwardly for breast cancer, validated by some independent databases. Accordingly, 31 validated driver genes, including four novel ones, were discovered. Subsequently, we detected cancer-related significantly enriched gene ontology terms and pathways, probable drug targets, two co-expressed modules associated significantly with several clinical features, such as number of positive lymph nodes, Nottingham prognostic index, and tumor stage, and two biologically distinct groups of BRCA patients. Data and source code of the case study can be downloaded at\u00a0<a href=\"https:\/\/github.com\/hauldhut\/drivergene\">https:\/\/github.com\/hauldhut\/drivergene<\/a>.<\/p>\n<p>Authors: Nguyen, Q.H. and Le, D.H.<\/p>\n<p>Read more about the article\u00a0<a href=\"https:\/\/www.nature.com\/articles\/s41598-020-77318-1\">here<\/a><\/p>\n<p>Read more about the author\u2019s publications\u00a0here<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Abstract The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":353,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[37],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v19.6.1 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data - Vinuni Research Website<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data - Vinuni Research Website\" \/>\n<meta property=\"og:description\" content=\"Abstract The cumulative of genes carrying mutations is vital for the establishment and development of cancer. However, this driver gene exploring research line has selected and used types of tools and models of analysis unsystematically and discretely. Also, the previous studies may have neglected low-frequency drivers and seldom predicted subgroup specificities of identified driver genes. [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/\" \/>\n<meta property=\"og:site_name\" content=\"Vinuni Research Website\" \/>\n<meta property=\"article:published_time\" content=\"2021-04-05T07:45:19+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-05T07:46:24+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/vinuni.edu.vn\/research\/wp-content\/uploads\/2022\/09\/Scientific-Reports-660x410-1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"660\" \/>\n\t<meta property=\"og:image:height\" content=\"410\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"phuong.ntn\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"phuong.ntn\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/\",\"url\":\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/\",\"name\":\"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data - Vinuni Research Website\",\"isPartOf\":{\"@id\":\"https:\/\/vinuni.edu.vn\/research\/#website\"},\"datePublished\":\"2021-04-05T07:45:19+00:00\",\"dateModified\":\"2022-09-05T07:46:24+00:00\",\"author\":{\"@id\":\"https:\/\/vinuni.edu.vn\/research\/#\/schema\/person\/d19200a9f0488a2d6374d8641ee8c085\"},\"breadcrumb\":{\"@id\":\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/vinuni.edu.vn\/research\/#website\",\"url\":\"https:\/\/vinuni.edu.vn\/research\/\",\"name\":\"Vinuni Research Website\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/vinuni.edu.vn\/research\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Person\",\"@id\":\"https:\/\/vinuni.edu.vn\/research\/#\/schema\/person\/d19200a9f0488a2d6374d8641ee8c085\",\"name\":\"phuong.ntn\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/vinuni.edu.vn\/research\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/678312306781d0830679d2c1a8a112f1?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/678312306781d0830679d2c1a8a112f1?s=96&d=mm&r=g\",\"caption\":\"phuong.ntn\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data - Vinuni Research Website","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:\/\/vinuni.edu.vn\/research\/improving-existing-analysis-pipeline-to-identify-and-analyze-cancer-driver-genes-using-multi-omics-data\/","og_locale":"en_US","og_type":"article","og_title":"Improving Existing Analysis Pipeline to Identify and Analyze Cancer Driver Genes Using Multi-omics Data - Vinuni Research Website","og_description":"Abstract The cumulative of genes carrying mutations is vital for the establishment and development of cancer. 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