The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.
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DOI：
10.1371/journal.pone.0050653
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Lecerf F
中科院分区：
文献类型：
--
作者：
Ouedraogo M;Bettembourg C;Bretaudeau A;Sallou O;Diot C;Demeure O;Lecerf F
将基因组结构和基因表达联系起来的研究激增，特别关注复制基因。虽然最初是由相同的序列复制的，但复制的基因在进化过程中会产生强烈的分化，并承担不同的功能或调节表达。然而，关于重复基因的功能和表达的信息仍然很少。因此，确定不同基因组中的重复基因组并描述其表达和功能将是研究界的一大兴趣。“重复基因数据库”（DGD）就是为此目的而开发的。DGD中有9种。对于每个物种，BLAST分析了与同一染色体上的基因对应的肽序列。根据这些两两BLAST比较和基因的基因组位置来定义重复基因组。对于每一组，当相关信息可用时，还计算基因表达数据之间的Pearson相关性和功能GO注释之间的语义相似性。duplicate Gene Database提供了多个物种共定位和重复基因的列表，并提供了可用的基因共表达水平和功能注释的语义相似值。将这些数据添加到重复基因组中，可以为基因表达分析提供有用的生物学信息。复制基因数据库可通过DGD网站（http://dgd.genouest.org）免费访问。
There 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. Nine 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. The 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.
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影响因子：
14.9
作者：
Dimmer EC;Huntley RP;Alam-Faruque Y;Sawford T;O'Donovan C;Martin MJ;Bely B;Browne P;Mun Chan W;Eberhardt R;Gardner M;Laiho K;Legge D;Magrane M;Pichler K;Poggioli D;Sehra H;Auchincloss A;Axelsen K;Blatter MC;Boutet E;Braconi-Quintaje S;Breuza L;Bridge A;Coudert E;Estreicher A;Famiglietti L;Ferro-Rojas S;Feuermann M;Gos A;Gruaz-Gumowski N;Hinz U;Hulo C;James J;Jimenez S;Jungo F;Keller G;Lemercier P;Lieberherr D;Masson P;Moinat M;Pedruzzi I;Poux S;Rivoire C;Roechert B;Schneider M;Stutz A;Sundaram S;Tognolli M;Bougueleret L;Argoud-Puy G;Cusin I;Duek-Roggli P;Xenarios I;Apweiler R
通讯作者：
Apweiler R
影响因子：
7
作者：
Bortoluzzi, S;Rampoldi, L;Danieli, GA
通讯作者：
Danieli, GA
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
4.4
作者：
Fukuoka Y;Inaoka H;Kohane IS
通讯作者：
Kohane IS
影响因子：
7
作者：
Huminiecki, L;Wolfe, KH
通讯作者：
Wolfe, KH