McCarthy F M, Bridges S M, Burgess S C
Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
Cytogenet Genome Res. 2007;117(1-4):278-87. doi: 10.1159/000103189.
The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics.
鸡的基因组已被测序，这与微阵列及其他功能基因组学技术一起，使得鸡的后基因组研究成为可能。然而，目前此类研究因缺乏基因组结构和功能注释而受到阻碍。生物本体已针对不同的注释需求开发出来，同时也为了便于数据共享和计算分析，但在鸡的研究中这些尚未得到最佳利用。在此我们讨论基因组注释和生物本体。我们特别关注基因本体（GO）、鸡的GO注释以及它们如何促进鸡的功能基因组学研究。GO是发展最为完善且应用最广泛的生物本体。它是功能注释的事实上的标准。尽管其在分析微阵列及其他功能基因组学数据方面至关重要，但相对较少的鸡基因产物有任何GO注释。即便有这些注释，鸡基因产物注释的平均质量（根据证据代码权重和注释深度定义）也远低于小鼠。此外，供鸡研究人员轻松快速使用GO的工具要么缺乏，要么难以使用。为解决所有这些问题，我们开发了ChickGO和AgBase。鸡的GO注释由密歇根州立大学 - AgBase和欧洲生物信息研究所 - GOA（EBI - GOA）的互补工作提供。AgBase的GO工具管道利用GO从微阵列及其他功能基因组学数据中得出功能和生物学意义。改进的基因组注释以及使用这些注释的工具不仅将使鸡研究群体受益，还将促进其他鸟类物种的研究及比较基因组学研究。
