The Duplicated Genes Database: Identification and Functional Annotation of Co-Localised Duplicated Genes across Genomes

BackgroundThere has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The ‘Duplicated Genes Database’ (DGD) was developed for this purpose. MethodologyNine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. ConclusionsThe Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.背景：近年来，关联基因组结构与基因表达的研究呈爆发式增长，其中尤以重复基因（duplicated genes）为研究焦点。重复基因虽最初源自同一序列，但在演化过程中可发生显著分化，进而获得不同功能或受到差异化的表达调控。然而，目前关于重复基因功能与表达的相关信息仍较为匮乏。在不同基因组中鉴定重复基因家族，并解析其表达模式与功能，是科研领域极具价值的研究方向，为此研发了「重复基因数据库（Duplicated Genes Database，DGD）」。方法：该数据库共收录9个物种的相关数据。针对每个物种，研究人员对位于同一染色体上的基因所对应的肽序列开展BLAST（Basic Local Alignment Search Tool）分析。基于两两BLAST比对结果与基因的基因组定位信息，定义重复基因家族。若存在可用的相关数据，还会对每个基因家族计算基因表达数据间的皮尔逊相关系数，以及功能基因本体（Gene Ontology，GO）注释间的语义相似度。结论：重复基因数据库为多个物种提供了共定位重复基因列表，并附带可用的基因共表达水平与功能注释语义相似度数值。将此类数据整合至重复基因家族中，可获得有助于基因表达分析的生物学信息。用户可通过DGD官网http://dgd.genouest.org免费访问该数据库。