Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a pro- tein- or gene-centric fashion. Unfortun...Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a pro- tein- or gene-centric fashion. Unfortunately, proteome-wide analysis of non-synonymous single- nucleotide variations （nsSNVs） is not easy to perform because information on nsSNVs and func- tionally important sites are not well integrated both within and between databases and their search engines. We have developed SNVDis that allows evaluation of proteome-wide nsSNV distribution in functional sites, domains and pathways. More specifically, we have integrated human-specific data from major variation databases （UniProtKB, dbSNP and COSMIC）, comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved Domain Database （CDD） and pathway information from Protein ANalysis THrough Evolutionary Relationships （PANTHER） and mapped all of them in a uniform and comprehensive way to the human reference proteome pro- vided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, which are extracted from a number of different sources, provides a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out whether there is an over- or under-representation of nsSNVs in specific domains, pathways or user-defined protein lists. The underlying datasets are updated once every 3 months. SNVDis is freely available at http：//hive.bio- chemistry.gwu.edu/tool/snvdis.展开更多
基金Support for this work came from The George Washington University funds to RMsupported in part by NIH (Grant No. U01 CA168926)an appointment to the Research Participation program at the Center for Biologics Evaluation and Research administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and the U.S. Food and Drug Administration
文摘Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a pro- tein- or gene-centric fashion. Unfortunately, proteome-wide analysis of non-synonymous single- nucleotide variations （nsSNVs） is not easy to perform because information on nsSNVs and func- tionally important sites are not well integrated both within and between databases and their search engines. We have developed SNVDis that allows evaluation of proteome-wide nsSNV distribution in functional sites, domains and pathways. More specifically, we have integrated human-specific data from major variation databases （UniProtKB, dbSNP and COSMIC）, comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved Domain Database （CDD） and pathway information from Protein ANalysis THrough Evolutionary Relationships （PANTHER） and mapped all of them in a uniform and comprehensive way to the human reference proteome pro- vided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, which are extracted from a number of different sources, provides a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out whether there is an over- or under-representation of nsSNVs in specific domains, pathways or user-defined protein lists. The underlying datasets are updated once every 3 months. SNVDis is freely available at http：//hive.bio- chemistry.gwu.edu/tool/snvdis.
