MARSweb: a fully automated web service for set-based association testing
Abstract Background Despite the successes in GWAS, there is still a large gap between the known heritability and the part explained by the SNPs identified by GWAS. Set-based analysis is one of the approaches that has tried to identify associations between multiple variants in a locus a trait, levera...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-02-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11356-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849768107346755584 |
|---|---|
| author | Taegun Kim Jaeseung Song Jong Wha J. Joo |
| author_facet | Taegun Kim Jaeseung Song Jong Wha J. Joo |
| author_sort | Taegun Kim |
| collection | DOAJ |
| description | Abstract Background Despite the successes in GWAS, there is still a large gap between the known heritability and the part explained by the SNPs identified by GWAS. Set-based analysis is one of the approaches that has tried to identify associations between multiple variants in a locus a trait, leveraging allelic heterogeneity to increase power in association testing. MARS is a set-based analysis method that integrates likelihood ratio test with a recently developed fine mapping technique to accurately account for causal status of variants in a risk locus. Unfortunately, due to its complex running process, time complexity, and the requirement of high-performance computing resources, it is not widely used. Results To address these issues, we proposed a fully automated web-based analysis service, MARSweb. By providing a web service, we minimized the effort required for initial configuration. Additionally, users can perform analyses by simply uploading their data without needing to familiarize themselves with intricate analysis procedures. Furthermore, it facilitates easier interpretation of results by integrating advanced visualization tools. We confirmed the performance of MARSweb by detecting eGenes and performing pathway analysis of the genes using a Yeast Dataset. Conclusions MARSweb is a web-based analysis service that fully automates set-based analysis. It offers an intuitive user interface, making complex analyses more accessible while significantly reducing processing time for enhanced efficiency. MARSweb is available for use at http://cblab.dongguk.edu/MARSweb and its source code is available at https://github.com/DGU-CBLAB/MARSweb . |
| format | Article |
| id | doaj-art-1f0f675c8f4548c28eeff237a136d801 |
| institution | DOAJ |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-1f0f675c8f4548c28eeff237a136d8012025-08-20T03:03:57ZengBMCBMC Genomics1471-21642025-02-012611910.1186/s12864-025-11356-9MARSweb: a fully automated web service for set-based association testingTaegun Kim0Jaeseung Song1Jong Wha J. Joo2Division of AI Software Convergence, Dongguk University-SeoulDepartment of Life Science, Dongguk University-SeoulDivision of AI Software Convergence, Dongguk University-SeoulAbstract Background Despite the successes in GWAS, there is still a large gap between the known heritability and the part explained by the SNPs identified by GWAS. Set-based analysis is one of the approaches that has tried to identify associations between multiple variants in a locus a trait, leveraging allelic heterogeneity to increase power in association testing. MARS is a set-based analysis method that integrates likelihood ratio test with a recently developed fine mapping technique to accurately account for causal status of variants in a risk locus. Unfortunately, due to its complex running process, time complexity, and the requirement of high-performance computing resources, it is not widely used. Results To address these issues, we proposed a fully automated web-based analysis service, MARSweb. By providing a web service, we minimized the effort required for initial configuration. Additionally, users can perform analyses by simply uploading their data without needing to familiarize themselves with intricate analysis procedures. Furthermore, it facilitates easier interpretation of results by integrating advanced visualization tools. We confirmed the performance of MARSweb by detecting eGenes and performing pathway analysis of the genes using a Yeast Dataset. Conclusions MARSweb is a web-based analysis service that fully automates set-based analysis. It offers an intuitive user interface, making complex analyses more accessible while significantly reducing processing time for enhanced efficiency. MARSweb is available for use at http://cblab.dongguk.edu/MARSweb and its source code is available at https://github.com/DGU-CBLAB/MARSweb .https://doi.org/10.1186/s12864-025-11356-9GWASAllelic heterogeneitySet-based analysisLikelihood ratio testWeb-based |
| spellingShingle | Taegun Kim Jaeseung Song Jong Wha J. Joo MARSweb: a fully automated web service for set-based association testing BMC Genomics GWAS Allelic heterogeneity Set-based analysis Likelihood ratio test Web-based |
| title | MARSweb: a fully automated web service for set-based association testing |
| title_full | MARSweb: a fully automated web service for set-based association testing |
| title_fullStr | MARSweb: a fully automated web service for set-based association testing |
| title_full_unstemmed | MARSweb: a fully automated web service for set-based association testing |
| title_short | MARSweb: a fully automated web service for set-based association testing |
| title_sort | marsweb a fully automated web service for set based association testing |
| topic | GWAS Allelic heterogeneity Set-based analysis Likelihood ratio test Web-based |
| url | https://doi.org/10.1186/s12864-025-11356-9 |
| work_keys_str_mv | AT taegunkim marswebafullyautomatedwebserviceforsetbasedassociationtesting AT jaeseungsong marswebafullyautomatedwebserviceforsetbasedassociationtesting AT jongwhajjoo marswebafullyautomatedwebserviceforsetbasedassociationtesting |