The Animal Functional Genomics Resource

对家养动物的研究具有重要的社会经济影响，包括支持和加速改进农业部门的动物(动物育种和动物健康)，通过提供动物模型为人类和兽医做出贡献，以及改善动物健康和福利。鸡也是所有其他鸟类的模型，因此在胚胎学和发育、神经生物学和行为以及自然种群的生态学和进化领域都很重要。基因组是有机体的全部DNA内容。为了使基因组序列有用，需要用DNA序列上的基因及其调控元件的位置来注释该序列。至少编码基因(即制造蛋白质的基因)的位置信息现在可用于许多经济上重要的饲养和同伴动物，世界许多地区正在努力增加我们对非编码区(即非编码RNA和调控元件)的了解。此外，新的DNA测序技术的出现意味着有可能对许多个体进行测序，比较它们在DNA序列和基因含量上的差异，并将这与它们的生理差异联系起来。也可以通过测序(“测序化验”)产生“功能”数据。功能序列数据告诉我们哪些基因是活跃的，哪些基因编码蛋白质，哪些基因编码调控RNA。它还可以告诉我们DNA序列中负责基因打开或关闭的其他功能，例如，在特定组织中或对信号分子做出反应。因此，功能序列数据非常重要，可以告诉我们个体DNA序列的差异如何影响基因活性，从而可能影响表型，如生产或抗病性状。有些DNA数据库包含养殖和伴生动物的功能数据，通常是原始数据(例如，序列读取)，然而，当这些数据经过质量检查和进一步处理时最有用，例如将其分配给特定的基因和转录本。如果世界各地的研究界向这些数据库提交更多数据，也会更好。我们提议的研究旨在查看公共DNA数据库中可用于这些动物的数据，并检查其质量。我们还将努力确保提交给数据库的未来数据集具有尽可能多的有用信息，例如品种、性别和组织类型等。我们还将为这些数据定义质量标准，并通过将不同项目的数据集汇集到一个可通过编程和通过网站访问的紧密集合来提高数据可发现性。

Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture (animal breeding and animal health), contributing to human and veterinary medicine by providing animal models, and improving animal health and welfare. The chicken also serves as a model for all other avian species, so is important in the fields of embryology and development, neurobiology and behaviour, and the ecology and evolution of natural populations.The genome is the entire DNA content of an organism. For the genome sequence to be useful, the sequence needs to be annotated with the location of genes and their regulatory elements along the DNA sequence. Information on the location of at least coding genes (that is, genes which make proteins) is now available for many economically important farmed and companion animals, and efforts are underway in many parts of the world to increase our knowledge of non-coding regions (i.e. non-coding RNAs and regulatory elements). In addition, the advent of new DNA sequencing technologies now mean that it is possible to sequence many individuals and compare their differences in DNA sequence and gene content and relate this to their physiological differences. It is also possible to generate 'functional' data by sequencing ("assay by sequencing"). Functional sequence data tells us about which genes are active, which genes code for proteins and which genes code for regulatory RNAs. It can also tell us about other features within the DNA sequence that are responsible for genes being switched on or off, for example, in specific tissues or in response to signaling molecules. Functional sequence data is therefore very important in informing us about how differences in the DNA sequence in individuals can affect gene activity and are therefore likely to affect phenotypes, such as production or disease resistance traits. Some DNA databases contain functional data for farmed and companion animals often in its raw form (e.g. sequence reads), however this data is most useful when it has been checked for quality and processed further, for example assigning it to specific genes and transcripts. It would also be preferable if more data were submitted to these databases from the research community around the world.Our proposed research aims to look at the data that is available for these animals in the public DNA databases, and check it for quality. We will also work to ensure that future datasets that are submitted to the databases have as much useful information associated with them as possible, for example, breed, sex and tissue type, etc. We will also define quality standards for such data and improve data discoverability by drawing together datasets from disparate projects into a cohesive collection that is accessible both programmatically and via a website.