Pengbo Wen1, Peng Xiao1, Junfeng Xia2. 1. Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, Anhui 230601, China and. 2. Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, Anhui 230601, China and Co-Innovation Center for Information Supply and Assurance Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China.
Abstract
MOTIVATION: Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. RESULTS: We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. AVAILABILITY AND IMPLEMENTATION: dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. CONTACT: jfxia@ahu.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. RESULTS: We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. AVAILABILITY AND IMPLEMENTATION: dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. CONTACT: jfxia@ahu.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jeffrey B S Gaither; Grant E Lammi; James L Li; David M Gordon; Harkness C Kuck; Benjamin J Kelly; James R Fitch; Peter White Journal: Gigascience Date: 2021-04-05 Impact factor: 6.524
Authors: Špela Mikec; Martin Šimon; Nicholas M Morton; Santosh S Atanur; Janez Konc; Peter Dovč; Simon Horvat; Tanja Kunej Journal: Mol Biol Rep Date: 2022-03-26 Impact factor: 2.742