A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data
Early diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in num...
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1204909/full |
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| author | Xiaoqin Huang Akhilesh K. Bajpai Jian Sun Fuyi Xu Fuyi Xu Lu Lu Lu Lu Siamak Yousefi Siamak Yousefi |
| author_facet | Xiaoqin Huang Akhilesh K. Bajpai Jian Sun Fuyi Xu Fuyi Xu Lu Lu Lu Lu Siamak Yousefi Siamak Yousefi |
| author_sort | Xiaoqin Huang |
| collection | DOAJ |
| description | Early diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in numerous transcriptome data analyses in order to identify subtypes and biomarkers of different diseases; however, its application in glaucoma biomarker discovery has not been previously reported. Our study applied NMF to extract latent representations of RNA-seq data from BXD mouse strains and sorted the genes based on a novel gene scoring method. The enrichment ratio of the glaucoma-reference genes, extracted from multiple relevant resources, was compared using both the classical differentially expressed gene (DEG) analysis and NMF methods. The complete pipeline was validated using an independent RNA-seq dataset. Findings showed our NMF method significantly improved the enrichment detection of glaucoma genes. The application of NMF with the scoring method showed great promise in the identification of marker genes for glaucoma. |
| first_indexed | 2024-03-13T06:01:21Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-13T06:01:21Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-9e3c077412814156b667b1f3be774de52023-06-12T16:10:50ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-06-011410.3389/fgene.2023.12049091204909A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq dataXiaoqin Huang0Akhilesh K. Bajpai1Jian Sun2Fuyi Xu3Fuyi Xu4Lu Lu5Lu Lu6Siamak Yousefi7Siamak Yousefi8Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United StatesIntegrated Data Science Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), Bethesda, MD, United StatesDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United StatesSchool of Pharmacy, Binzhou Medical University, Yantai, Shandong, ChinaDepartment of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United StatesEarly diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in numerous transcriptome data analyses in order to identify subtypes and biomarkers of different diseases; however, its application in glaucoma biomarker discovery has not been previously reported. Our study applied NMF to extract latent representations of RNA-seq data from BXD mouse strains and sorted the genes based on a novel gene scoring method. The enrichment ratio of the glaucoma-reference genes, extracted from multiple relevant resources, was compared using both the classical differentially expressed gene (DEG) analysis and NMF methods. The complete pipeline was validated using an independent RNA-seq dataset. Findings showed our NMF method significantly improved the enrichment detection of glaucoma genes. The application of NMF with the scoring method showed great promise in the identification of marker genes for glaucoma.https://www.frontiersin.org/articles/10.3389/fgene.2023.1204909/fullglaucomaRNA-seqDEGNMFBXD strainspathway analysis |
| spellingShingle | Xiaoqin Huang Akhilesh K. Bajpai Jian Sun Fuyi Xu Fuyi Xu Lu Lu Lu Lu Siamak Yousefi Siamak Yousefi A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data Frontiers in Genetics glaucoma RNA-seq DEG NMF BXD strains pathway analysis |
| title | A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data |
| title_full | A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data |
| title_fullStr | A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data |
| title_full_unstemmed | A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data |
| title_short | A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data |
| title_sort | new gene scoring method for uncovering novel glaucoma related genes using non negative matrix factorization based on rna seq data |
| topic | glaucoma RNA-seq DEG NMF BXD strains pathway analysis |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1204909/full |
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