Dawson Harry D, Chen Celine, Gaynor Brady, Shao Jonathan, Urban Joseph F
United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA.
United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab, Beltsville, MD, 20705, USA.
BMC Genomics. 2017 Aug 22;18(1):643. doi: 10.1186/s12864-017-4009-7.
The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.
The process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.
This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.
在过去十年中，猪在生物医学研究中的使用急剧增加。为了便于使用人类和啮齿动物模型进行研究，已经开发了各种基因组和蛋白质组数据库。然而，当前的猪基因数据库缺乏强大的注释，无法用于研究与人类研究相关的猪模型以及与啮齿动物模型进行比较评估。此外，由于主要依赖基于机器的注释，它们包含大量错误。为了解决这些不足，我们进行了一项基于文献的全面调查，以确定某些在人类、小鼠或猪中已证明具有功能的选定基因。
该过程确定了13054个候选人类、牛、小鼠或大鼠基因/蛋白质，通过搜索多个猪基因信息在线来源来选择潜在的猪同源物。猪转化研究数据库（http://www.ars.usda.gov/Services/docs.htm?docid=6065）中的数据得到了5800多篇参考文献的支持，每个条目包含65个数据字段，包括9700多条全长（5'和3'）明确的猪序列、2400多个实时PCR检测以及1700多种抗体的反应性信息。它还包含2200多个基因的基因和/或蛋白质表达数据，并识别和纠正了5337个猪基因的8187个错误（基因重复、错误组装、错误注释和错误的物种分配）。
该数据库是针对任何单一兽医物种的最大的人工策划数据库，在将基因表达与基因功能联系起来、识别相关基因途径以及将数据与其他猪基因数据库连接方面，在猪基因数据库中是独一无二的。该数据库首次全面描述了三个主要的超家族或功能相关的蛋白质组（分化簇（CD）标记基因、溶质载体超家族、ATP结合盒超家族），并对猪微小RNA进行了比较描述。
