{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T10:44:01Z","timestamp":1788518641942,"version":"build-2803163510"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T00:00:00Z","timestamp":1702598400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81970414"],"award-info":[{"award-number":["81970414"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Abdominal aortic aneurysm (AAA), an extremely dangerous vascular disease with high mortality, causes massive internal bleeding due to aneurysm rupture. To boost the research on AAA, efforts should be taken to organize and link the information about AAA-related genes and their functions. Currently, most researchers screen through genetic databases manually, which is cumbersome and time-consuming. Here, we developed \u201cAAAKB\u201d a manually curated knowledgebase containing genes, SNPs and pathways associated with AAA. In order to facilitate researchers to further explore the mechanism network of AAA, AAAKB provides predicted genes that are potentially associated with AAA. The prediction is based on the protein interaction information of genes collected in the database, and the random forest algorithm (RF) is used to build the prediction model. Some of these predicted genes are differentially expressed in patients with AAA, and some have been reported to play a role in other cardiovascular diseases, illustrating the utility of the knowledgebase in predicting novel genes. Also, AAAKB integrates a protein interaction visualization tool to quickly determine the shortest paths between target proteins. As the first knowledgebase to provide a comprehensive catalog of AAA-related genes, AAAKB will be an ideal research platform for AAA. Database URL: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.lqlgroup.cn:3838\/AAAKB\/\" xlink:type=\"simple\">http:\/\/www.lqlgroup.cn:3838\/AAAKB\/<\/jats:ext-link>.<\/jats:p>","DOI":"10.1371\/journal.pone.0289966","type":"journal-article","created":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T18:31:41Z","timestamp":1702665101000},"page":"e0289966","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["AAAKB: A manually curated database for tracking and predicting genes of Abdominal aortic aneurysm (AAA)"],"prefix":"10.1371","volume":"18","author":[{"given":"Di","family":"Yao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuyuan","family":"Mei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wangyang","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingyu","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiulun","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4330-7657","authenticated-orcid":true,"given":"Zhiguang","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,12,15]]},"reference":[{"key":"pone.0289966.ref001","first-page":"5","article-title":"Abdominal aortic aneurysm: pictorial review of common appearances and complications","author":"Y Kumar","year":"2017","journal-title":"Annals of Translational Medicine"},{"key":"pone.0289966.ref002","doi-asserted-by":"crossref","first-page":"3650","DOI":"10.18632\/aging.101702","article-title":"Abdominal aortic aneurysm in aged population","volume":"10","author":"R Umebayashi","year":"2018","journal-title":"Aging (Albany NY)"},{"key":"pone.0289966.ref003","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/joim.12958","article-title":"Lack of an effective drug therapy for abdominal aortic aneurysm","volume":"288","author":"J Golledge","year":"2020","journal-title":"J Intern Med"},{"key":"pone.0289966.ref004","doi-asserted-by":"crossref","first-page":"2619","DOI":"10.1182\/blood-2017-08-743237","article-title":"Antithrombotic therapy in abdominal aortic aneurysm: beneficial or detrimental?","volume":"132","author":"SJ Cameron","year":"2018","journal-title":"Blood"},{"key":"pone.0289966.ref005","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/s41569-018-0114-9","article-title":"Abdominal aortic aneurysm: update on pathogenesis and medical treatments","volume":"16","author":"J. Golledge","year":"2019","journal-title":"Nat Rev Cardiol"},{"key":"pone.0289966.ref006","doi-asserted-by":"crossref","first-page":"191","DOI":"10.3390\/life12020191","article-title":"Abdominal Aortic Aneurysm Formation with a Focus on Vascular Smooth Muscle Cells","volume":"12","author":"G Qian","year":"2022","journal-title":"Life"},{"key":"pone.0289966.ref007","doi-asserted-by":"crossref","first-page":"221","DOI":"10.2174\/1874192401004010221","article-title":"Experimental Models of Abdominal Aortic Aneurysms","volume":"4","author":"JC Tsui","year":"2010","journal-title":"TOCMJ"},{"key":"pone.0289966.ref008","doi-asserted-by":"crossref","first-page":"7250","DOI":"10.3390\/ijms21197250","article-title":"Risk Factors and Mouse Models of Abdominal Aortic Aneurysm Rupture","volume":"21","author":"S Murali Krishna","year":"2020","journal-title":"IJMS"},{"key":"pone.0289966.ref009","doi-asserted-by":"crossref","first-page":"e1008903","DOI":"10.1371\/journal.pgen.1008903","article-title":"Protein-Protein interactions uncover candidate \u201ccore genes\u201d within omnigenic disease networks","volume":"16","author":"A Ratnakumar","year":"2020","journal-title":"PLoS Genet"},{"key":"pone.0289966.ref010","doi-asserted-by":"crossref","first-page":"596794","DOI":"10.3389\/fgene.2021.596794","article-title":"Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity","volume":"12","author":"Y Zhang","year":"2021","journal-title":"Front Genet"},{"issue":"4","key":"pone.0289966.ref011","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1186\/s12864-016-2795-y","article-title":"Predicting diabetes mellitus genes via protein-protein interaction and protein subcellular localization information","volume":"17","author":"X Tang","year":"2016","journal-title":"BMC Genomics"},{"key":"pone.0289966.ref012","doi-asserted-by":"crossref","first-page":"bbab036","DOI":"10.1093\/bib\/bbab036","article-title":"A survey on computational models for predicting protein-protein interactions","volume":"22","author":"L Hu","year":"2021","journal-title":"Brief Bioinform"},{"key":"pone.0289966.ref013","doi-asserted-by":"crossref","first-page":"bbab111","DOI":"10.1093\/bib\/bbab111","article-title":"SMMPPI: a machine learning-based approach for prediction of modulators of protein-protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2","volume":"22","author":"P Gupta","year":"2021","journal-title":"Brief Bioinform"},{"key":"pone.0289966.ref014","doi-asserted-by":"crossref","first-page":"328","DOI":"10.3389\/fgene.2020.00328","article-title":"Predicting the Disease Genes of Multiple Sclerosis Based on Network Representation Learning","volume":"11","author":"H Liu","year":"2020","journal-title":"Front Genet"},{"key":"pone.0289966.ref015","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"ME Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pone.0289966.ref016","doi-asserted-by":"crossref","first-page":"4311","DOI":"10.1038\/s41467-020-18088-2","article-title":"Lung-derived HMGB1 is detrimental for vascular remodeling of metabolically imbalanced arterial macrophages","volume":"11","author":"L Boytard","year":"2020","journal-title":"Nat Commun"},{"key":"pone.0289966.ref017","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Y Zhou","year":"2019","journal-title":"Nat Commun"},{"key":"pone.0289966.ref018","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1093\/cvr\/cvy174","article-title":"Diabetes and aortic aneurysm: current state of the art","volume":"114","author":"J Raffort","year":"2018","journal-title":"Cardiovascular Research"},{"key":"pone.0289966.ref019","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bib\/bbp057","article-title":"Toward the dynamic interactome: it\u2019s about time","volume":"11","author":"TM Przytycka","year":"2010","journal-title":"Brief Bioinform"},{"key":"pone.0289966.ref020","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/msb4100129","article-title":"Network-based prediction of protein function","volume":"3","author":"R Sharan","year":"2007","journal-title":"Mol Syst Biol"},{"issue":"12","key":"pone.0289966.ref021","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2105-10-S12-S8","article-title":"Identification of functionally related genes using data mining and data integration: a breast cancer case study","volume":"10","author":"E Mosca","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"pone.0289966.ref022","doi-asserted-by":"crossref","first-page":"8685","DOI":"10.1073\/pnas.0701361104","article-title":"The human disease network","volume":"104","author":"K-I Goh","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0289966.ref023","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1161\/ATVBAHA.114.304723","article-title":"Regulation of Csf1r and Bcl6 in macrophages mediates the stage-specific effects of microRNA-155 on atherosclerosis","volume":"35","author":"Y Wei","year":"2015","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"pone.0289966.ref024","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1093\/cvr\/cvp119","article-title":"Impaired binding of ZASP\/Cypher with phosphoglucomutase 1 is associated with dilated cardiomyopathy","volume":"83","author":"T Arimura","year":"2009","journal-title":"Cardiovasc Res"},{"key":"pone.0289966.ref025","doi-asserted-by":"crossref","first-page":"10641","DOI":"10.3390\/ijms221910641","article-title":"Pleiotropic Effects of Functional MUC1 Variants on Cardiometabolic, Renal, and Hematological Traits in the Taiwanese Population","volume":"22","author":"M-S Teng","year":"2021","journal-title":"Int J Mol Sci"},{"key":"pone.0289966.ref026","doi-asserted-by":"crossref","first-page":"948002","DOI":"10.3389\/fcvm.2022.948002","article-title":"The diagnostic significance of integrating m6A modification and immune microenvironment features based on bioinformatic investigation in aortic dissection","volume":"9","author":"R Guo","year":"2022","journal-title":"Front Cardiovasc Med"},{"key":"pone.0289966.ref027","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1093\/ndt\/gfv048","article-title":"Emerging role of post-translational modifications in chronic kidney disease and cardiovascular disease","volume":"30","author":"PR Gajjala","year":"2015","journal-title":"Nephrology Dialysis Transplantation"},{"key":"pone.0289966.ref028","doi-asserted-by":"crossref","first-page":"3795","DOI":"10.1111\/jcmm.14330","article-title":"The role of post\u2010translational modifications in cardiac hypertrophy","volume":"23","author":"K Yan","year":"2019","journal-title":"J Cell Mol Med"},{"key":"pone.0289966.ref029","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1752-0509-9-S1-S1","article-title":"cisPath: an R\/Bioconductor package for cloud users for visualization and management of functional protein interaction networks","volume":"9","author":"L Wang","year":"2015","journal-title":"BMC Syst Biol"},{"key":"pone.0289966.ref030","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"A Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pone.0289966.ref031","doi-asserted-by":"crossref","first-page":"D134","DOI":"10.1093\/nar\/gkaa692","article-title":"m6A-Atlas: a comprehensive knowledgebase for unraveling the N 6-methyladenosine (m6A) epitranscriptome","volume":"49","author":"Y Tang","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"pone.0289966.ref032","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13046-022-02285-6","article-title":"A reciprocal feedback between N6-methyladenosine reader YTHDF3 and lncRNA DICER1-AS1 promotes glycolysis of pancreatic cancer through inhibiting maturation of miR-5586-5p","volume":"41","author":"Y Hu","year":"2022","journal-title":"J Exp Clin Cancer Res"},{"key":"pone.0289966.ref033","doi-asserted-by":"crossref","first-page":"e0140888","DOI":"10.1371\/journal.pone.0140888","article-title":"Predicting Abdominal Aortic Aneurysm Target Genes by Level-2 Protein-Protein Interaction","volume":"10","author":"K Zhang","year":"2015","journal-title":"PLOS ONE"},{"key":"pone.0289966.ref034","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM\u00ae), an online catalog of human genes and genetic disorders","volume":"43","author":"JS Amberger","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"pone.0289966.ref035","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1161\/CIRCRESAHA.118.312436","article-title":"Genetics of Thoracic and Abdominal Aortic Diseases: Aneurysms, Dissections, and Ruptures","volume":"124","author":"A Pinard","year":"2019","journal-title":"Circ Res"},{"key":"pone.0289966.ref036","first-page":"e935006-1","article-title":"Studies Related to Ruptured Abdominal Aortic Aneurysms in the Past 10 Years (2011\u20132020): A Bibliometric Analysis","volume":"28","author":"B Teng","year":"2022","journal-title":"Med Sci Monit"},{"key":"pone.0289966.ref037","doi-asserted-by":"crossref","first-page":"e83","DOI":"10.1161\/ATVBAHA.119.312000","article-title":"Updates of Recent Aortic Aneurysm Research","volume":"39","author":"FM Davis","year":"2019","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"pone.0289966.ref038","doi-asserted-by":"crossref","first-page":"e83","DOI":"10.1161\/ATVBAHA.119.312000","article-title":"Recent Highlights of ATVB Updates of Recent Aortic Aneurysm Research","volume":"39","author":"FM Davis","year":"2019","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"pone.0289966.ref039","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1038\/s41584-018-0005-9","article-title":"Biomarkers as drug development tools: discovery, validation, qualification and use","volume":"14","author":"VB Kraus","year":"2018","journal-title":"Nat Rev Rheumatol"},{"key":"pone.0289966.ref040","first-page":"111","article-title":"Pharmacogenetics: An Important Part of Drug Development with A Focus on Its Application","volume":"1","author":"J Oates","year":"2018","journal-title":"Int J Biomed Investig"},{"key":"pone.0289966.ref041","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/978-3-030-05542-4_2","article-title":"The Role of Biomarkers in Alzheimer\u2019s Disease Drug Development","volume":"1118","author":"J. Cummings","year":"2019","journal-title":"Adv Exp Med Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0289966","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T18:32:08Z","timestamp":1702665128000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0289966"}},"subtitle":[],"editor":[{"given":"Vincenzo","family":"Bonnici","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,15]]},"references-count":41,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2023,12,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0289966","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,15]]}}}