{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:35Z","timestamp":1753875755000,"version":"3.41.2"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,8]],"date-time":"2022-12-08T00:00:00Z","timestamp":1670457600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U24HG006941","U2RTW010679"],"award-info":[{"award-number":["U24HG006941","U2RTW010679"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into research insights and clinical benefits such as the effectiveness of strategies for disease screening, treatment and prevention. However, the setup of pGWAS (pGWAS) tools can be quite complicated, and it mostly requires big data. The challenge however is, scientists are required to have sufficient experience with several of these technically complex and complicated tools in order to complete the pGWAS analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present SysBiolPGWAS, a pGWAS web application that provides a comprehensive functionality for biologists and non-bioinformaticians to conduct several pGWAS analyses to overcome the above challenges. It provides unique functionalities for analysis involving multi-omics datasets and visualization using various bioinformatics tools. SysBiolPGWAS provides access to individual pGWAS tools and a novel custom pGWAS pipeline that integrates several individual pGWAS tools and data. The SysBiolPGWAS app was developed to be a one-stop shop for pGWAS analysis. It targets researchers in the area of the human genome and performs its analysis mainly in the autosomal chromosomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SysBiolPGWAS web app was developed using JavaScript\/TypeScript web frameworks and is available at: https:\/\/spgwas.waslitbre.org\/. All codes are available in this GitHub repository https:\/\/github.com\/covenant-university-bioinformatics.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac791","type":"journal-article","created":{"date-parts":[[2022,12,8]],"date-time":"2022-12-08T12:53:15Z","timestamp":1670503995000},"source":"Crossref","is-referenced-by-count":3,"title":["SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4448-7829","authenticated-orcid":false,"given":"Oluwadamilare","family":"Falola","sequence":"first","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6874-2543","authenticated-orcid":false,"given":"Yagoub","family":"Adam","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olabode","family":"Ajayi","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape , Cape Town 7535, Republic of South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judit","family":"Kumuthini","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape , Cape Town 7535, Republic of South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suraju","family":"Adewale","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abayomi","family":"Mosaku","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaimae","family":"Samtal","sequence":"additional","affiliation":[{"name":"Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University , Fez 30000, Morocco"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Glory","family":"Adebayo","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Biological Sciences, Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jerry","family":"Emmanuel","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Computer & Information Sciences, Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Milaine S S","family":"Tchamga","sequence":"additional","affiliation":[{"name":"African Institute for Mathematical Sciences (AIMS) , Muizenberg, Cape Town 7945, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Udochukwu","family":"Erondu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Landmark University , Omu-Aran, Kwara State 251103, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5838-8843","authenticated-orcid":false,"given":"Adebayo","family":"Nehemiah","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Landmark University , Omu-Aran, Kwara State 251103, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suraj","family":"Rasaq","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Landmark University , Omu-Aran, Kwara State 251103, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary","family":"Ajayi","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Landmark University , Omu-Aran, Kwara State 251103, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bola","family":"Akanle","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Center for System and Information Services, Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olaleye","family":"Oladipo","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Center for System and Information Services, Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Itunuoluwa","family":"Isewon","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Computer & Information Sciences, Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marion","family":"Adebiyi","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Computer Science, Landmark University , Omu-Aran, Kwara State 251103, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5476-4992","authenticated-orcid":false,"given":"Jelili","family":"Oyelade","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Computer & Information Sciences, Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1390-2359","authenticated-orcid":false,"given":"Ezekiel","family":"Adebiyi","sequence":"additional","affiliation":[{"name":"Covenant University Bioinformatics Research (CUBRe), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Department of Computer & Information Sciences, Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University , Ota, Ogun State 112104, Nigeria"},{"name":"Applied Bioinformatics Division, German Cancer Research Center (DKFZ) , Heidelberg 69120, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,8]]},"reference":[{"key":"2023010805405926600_btac791-B1","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1101\/gr.137323.112","article-title":"Annotation of functional variation in personal genomes using RegulomeDB","volume":"22","author":"Boyle","year":"2012","journal-title":"Genome Res"},{"key":"2023010805405926600_btac791-B2","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023010805405926600_btac791-B3","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/s13059-016-1112-z","article-title":"DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles","volume":"17","author":"Chen","year":"2016","journal-title":"Genome Biol"},{"key":"2023010805405926600_btac791-B4","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1038\/s41596-020-0353-1","article-title":"Tutorial: a guide to performing polygenic risk score analyses","volume":"15","author":"Choi","year":"2020","journal-title":"Nat. Protoc"},{"key":"2023010805405926600_btac791-B5","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1101\/gr.3577405","article-title":"Distribution and intensity of constraint in mammalian genomic sequence","volume":"15","author":"Cooper","year":"2005","journal-title":"Genome Res"},{"key":"2023010805405926600_btac791-B6","doi-asserted-by":"crossref","first-page":"e1001025","DOI":"10.1371\/journal.pcbi.1001025","article-title":"Identifying a high fraction of the human genome to be under selective constraint using GERP++","volume":"6","author":"Davydov","year":"2010","journal-title":"PLoS Comput. Biol"},{"key":"2023010805405926600_btac791-B7","doi-asserted-by":"crossref","first-page":"e1004219","DOI":"10.1371\/journal.pcbi.1004219","article-title":"MAGMA: generalized gene-set analysis of GWAS data","volume":"11","author":"de Leeuw","year":"2015","journal-title":"PLoS Comput. Biol"},{"key":"2023010805405926600_btac791-B8","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.ajhg.2018.04.002","article-title":"The post-GWAS era: from association to function","volume":"102","author":"Gallagher","year":"2018","journal-title":"Am. J. Hum. Genet"},{"key":"2023010805405926600_btac791-B9","doi-asserted-by":"crossref","first-page":"D853","DOI":"10.1093\/nar\/gky1095","article-title":"The UCSC genome browser database: 2019 update","volume":"47","author":"Haeussler","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023010805405926600_btac791-B10","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/ng.3477","article-title":"A spectral approach integrating functional genomic annotations for coding and noncoding variants","volume":"48","author":"Ionita-Laza","year":"2016","journal-title":"Nat. Genet"},{"key":"2023010805405926600_btac791-B11","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/ng.2892","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat. Genet"},{"key":"2023010805405926600_btac791-B12","doi-asserted-by":"crossref","first-page":"e1004714","DOI":"10.1371\/journal.pcbi.1004714","article-title":"Fast and rigorous computation of gene and pathway scores from SNP-Based summary statistics","volume":"12","author":"Lamparter","year":"2016","journal-title":"PLoS Comput. Biol"},{"key":"2023010805405926600_btac791-B13","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13073-020-00803-9","article-title":"dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs","volume":"12","author":"Liu","year":"2020","journal-title":"Genome Med"},{"key":"2023010805405926600_btac791-B14","doi-asserted-by":"crossref","first-page":"lqaa054","DOI":"10.1093\/nargab\/lqaa054","article-title":"Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data","volume":"2","author":"Luu","year":"2020","journal-title":"NAR Genom. Bioinform"},{"key":"2023010805405926600_btac791-B15","doi-asserted-by":"crossref","first-page":"100004","DOI":"10.1016\/j.xgen.2021.100004","article-title":"Workshop proceedings: GWAS summary statistics standards and sharing","volume":"1","author":"MacArthur","year":"2021","journal-title":"Cell Genom"},{"key":"2023010805405926600_btac791-B16","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1038\/ng.2435","article-title":"Bayesian refinement of association signals for 14 loci in 3 common diseases","volume":"44","author":"Maller","year":"2012","journal-title":"Nat. Genet"},{"key":"2023010805405926600_btac791-B17","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/s41588-019-0367-1","article-title":"Probabilistic fine-mapping of transcriptome-wide association studies","volume":"51","author":"Mancuso","year":"2019","journal-title":"Nat. Genet"},{"key":"2023010805405926600_btac791-B18","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2023010805405926600_btac791-B19","doi-asserted-by":"crossref","first-page":"3842","DOI":"10.1093\/bioinformatics\/btz138","article-title":"deTS: tissue-specific enrichment analysis to decode tissue specificity","volume":"35","author":"Pei","year":"2019","journal-title":"Bioinformatics"},{"key":"2023010805405926600_btac791-B20","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1016\/j.ajhg.2019.11.001","article-title":"Making the most of clumping and thresholding for polygenic scores","volume":"105","author":"Priv\u00e9","year":"2019","journal-title":"Am. J. Hum. Genet"},{"key":"2023010805405926600_btac791-B21","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1093\/bioinformatics\/btu703","article-title":"DANN: a deep learning approach for annotating the pathogenicity of genetic variants","volume":"31","author":"Quang","year":"2015","journal-title":"Bioinformatics"},{"key":"2023010805405926600_btac791-B22","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gky1016","article-title":"CADD: predicting the deleteriousness of variants throughout the human genome","volume":"47","author":"Rentzsch","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023010805405926600_btac791-B23","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nmeth.2832","article-title":"Functional annotation of noncoding sequence variants","volume":"11","author":"Ritchie","year":"2014","journal-title":"Nat. Methods"},{"key":"2023010805405926600_btac791-B24","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/s41576-018-0016-z","article-title":"From genome-wide associations to candidate causal variants by statistical fine-mapping","volume":"19","author":"Schaid","year":"2018","journal-title":"Nat. Rev. Genet"},{"key":"2023010805405926600_btac791-B25","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/s41576-019-0127-1","article-title":"Benefits and limitations of genome-wide association studies","volume":"20","author":"Tam","year":"2019","journal-title":"Nat. Rev. Genet"},{"key":"2023010805405926600_btac791-B26","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1093\/bioinformatics\/btz669","article-title":"Regulatory annotation of genomic intervals based on tissue-specific expression QTLs","volume":"36","author":"Xu","year":"2020","journal-title":"Bioinformatics"},{"key":"2023010805405926600_btac791-B27","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1086\/519024","article-title":"A Bayesian measure of the probability of false discovery in genetic epidemiology studies","volume":"81","author":"Wakefield","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023010805405926600_btac791-B28","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/gepi.20359","article-title":"Bayes factors for genome-wide association studies: comparison with P-values","volume":"33","author":"Wakefield","year":"2009","journal-title":"Genet. Epidemiol"},{"key":"2023010805405926600_btac791-B29","doi-asserted-by":"crossref","first-page":"e1009440","DOI":"10.1371\/journal.pgen.1009440","article-title":"A more accurate method for colocalization analysis allowing for multiple causal variants","volume":"17","author":"Wallace","year":"2021","journal-title":"PLoS Genet"},{"key":"2023010805405926600_btac791-B30","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023010805405926600_btac791-B31","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/s00281-021-00902-8","article-title":"Methods for statistical fine-mapping and their applications to auto-immune diseases","volume":"44","author":"Wang","year":"2022","journal-title":"Semin. Immunopathol"},{"key":"2023010805405926600_btac791-B32","doi-asserted-by":"crossref","first-page":"D877","DOI":"10.1093\/nar\/gkv1340","article-title":"HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease","volume":"44","author":"Ward","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023010805405926600_btac791-B33","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/s41467-018-03371-0","article-title":"Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits","volume":"9","author":"Wu","year":"2018","journal-title":"Nat. Commun"},{"key":"2023010805405926600_btac791-B34","first-page":"97","article-title":"haploR: an R package for querying web-based annotation tools","volume":"6","author":"Zhbannikov","year":"2017","journal-title":"F1000Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac791\/48181900\/btac791.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac791\/48520836\/btac791.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac791\/48520836\/btac791.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T05:41:21Z","timestamp":1673156481000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac791\/6883906"}},"subtitle":[],"editor":[{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,12,8]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac791","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,12,8]]},"article-number":"btac791"}}