Ayroles Julien F, Laflamme Brooke A, Stone Eric A, Wolfner Mariana F, Mackay Trudy F C
Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA.
Genet Res (Camb). 2011 Dec;93(6):387-95. doi: 10.1017/S0016672311000346.
Predicting functional gene annotations remains a significant challenge, even in well-annotated genomes such as yeast and Drosophila. One promising, high-throughput method for gene annotation is to use correlated gene expression patterns to annotate target genes based on the known function of focal genes. The Drosophila melanogaster transcriptome varies genetically among wild-derived inbred lines, with strong genetic correlations among the transcripts. Here, we leveraged the genetic correlations in gene expression among known seminal fluid protein (SFP) genes and the rest of the genetically varying transcriptome to identify 176 novel candidate SFPs (cSFPs). We independently validated the correlation in gene expression between seven of the cSFPs and a known SFP gene, as well as expression in male reproductive tissues. We argue that this method can be extended to other systems for which information on genetic variation in gene expression is available.
预测功能基因注释仍然是一项重大挑战，即使在诸如酵母和果蝇等注释完善的基因组中也是如此。一种有前景的高通量基因注释方法是利用相关基因表达模式，根据焦点基因的已知功能来注释目标基因。黑腹果蝇转录组在野生近交系中存在遗传差异，转录本之间存在很强的遗传相关性。在这里，我们利用已知精液蛋白（SFP）基因与其余遗传变异转录组之间的基因表达遗传相关性，鉴定出176个新的候选SFP（cSFP）。我们独立验证了7个cSFP与一个已知SFP基因之间的基因表达相关性，以及它们在雄性生殖组织中的表达。我们认为，这种方法可以扩展到其他有基因表达遗传变异信息的系统。
