GTExome: Modeling commonly expressed missense mutations in the human genome.
A web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0303604 |
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| author | Jill Hoffman Henry Tan Clara Sandoval-Cooper Kaelyn de Villiers Scott M Reed |
| author_facet | Jill Hoffman Henry Tan Clara Sandoval-Cooper Kaelyn de Villiers Scott M Reed |
| author_sort | Jill Hoffman |
| collection | DOAJ |
| description | A web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly expressed missense mutations in proteins from a wide range of tissue types can be selected and assessed for modeling suitability. Information about the consequences of each mutation is provided to the user including if disulfide bonds, hydrogen bonds, or salt bridges are broken, buried prolines introduced, buried charges are created or lost, charge is swapped, a buried glycine is replaced, or if the residue that would be removed is a proline in the cis configuration. Also, if the mutation site is in a binding pocket the number of pockets and their volumes are reported. The user can assess this information and then select from available experimental or computationally predicted structures of native proteins to create, visualize, and download a model of the mutated protein using Fast and Accurate Side-chain Protein Repacking (FASPR). For AlphaFold modeled proteins, confidence scores for native proteins are provided. Using this tool, we explored a set of 9,666 common missense mutations from a variety of tissues from GTEx and show that most mutations can be modeled using this tool to facilitate studies of protein-protein and protein-drug interactions. The open-source tool is freely available at https://pharmacogenomics.clas.ucdenver.edu/gtexome/. |
| format | Article |
| id | doaj-art-b4b3e219ae024db486d573c7fb3750b7 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-b4b3e219ae024db486d573c7fb3750b72025-01-17T05:32:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-01195e030360410.1371/journal.pone.0303604GTExome: Modeling commonly expressed missense mutations in the human genome.Jill HoffmanHenry TanClara Sandoval-CooperKaelyn de VilliersScott M ReedA web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly expressed missense mutations in proteins from a wide range of tissue types can be selected and assessed for modeling suitability. Information about the consequences of each mutation is provided to the user including if disulfide bonds, hydrogen bonds, or salt bridges are broken, buried prolines introduced, buried charges are created or lost, charge is swapped, a buried glycine is replaced, or if the residue that would be removed is a proline in the cis configuration. Also, if the mutation site is in a binding pocket the number of pockets and their volumes are reported. The user can assess this information and then select from available experimental or computationally predicted structures of native proteins to create, visualize, and download a model of the mutated protein using Fast and Accurate Side-chain Protein Repacking (FASPR). For AlphaFold modeled proteins, confidence scores for native proteins are provided. Using this tool, we explored a set of 9,666 common missense mutations from a variety of tissues from GTEx and show that most mutations can be modeled using this tool to facilitate studies of protein-protein and protein-drug interactions. The open-source tool is freely available at https://pharmacogenomics.clas.ucdenver.edu/gtexome/.https://doi.org/10.1371/journal.pone.0303604 |
| spellingShingle | Jill Hoffman Henry Tan Clara Sandoval-Cooper Kaelyn de Villiers Scott M Reed GTExome: Modeling commonly expressed missense mutations in the human genome. PLoS ONE |
| title | GTExome: Modeling commonly expressed missense mutations in the human genome. |
| title_full | GTExome: Modeling commonly expressed missense mutations in the human genome. |
| title_fullStr | GTExome: Modeling commonly expressed missense mutations in the human genome. |
| title_full_unstemmed | GTExome: Modeling commonly expressed missense mutations in the human genome. |
| title_short | GTExome: Modeling commonly expressed missense mutations in the human genome. |
| title_sort | gtexome modeling commonly expressed missense mutations in the human genome |
| url | https://doi.org/10.1371/journal.pone.0303604 |
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