The Animal Functional Genomics Resource

动物功能基因组学资源

• 批准号: BB/N019563/1
• 负责人: Paul Flicek
• 金额: $ 69.28万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN019563%2F1
• 关键词: Animal; Functional; Genomics; Resource

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.

对驯养动物的研究具有重要的社会经济影响，包括支撑和加速农业动物部门（动物育种和动物健康）的改进，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。鸡还可以作为所有其他鸟类物种的模型，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和进化领域具有重要意义。基因组是生物体的全部 DNA 内容。为了使基因组序列有用，需要用基因及其调控元件沿 DNA 序列的位置对该序列进行注释。对于许多经济上重要的养殖动物和伴侣动物来说，至少可以获得编码基因（即制造蛋白质的基因）位置的信息，并且世界许多地方正在努力增加我们对非编码区域的了解。即非编码 RNA 和调控元件）。此外，新DNA测序技术的出现意味着可以对许多个体进行测序并比较他们在DNA序列和基因内容方面的差异，并将其与他们的生理差异联系起来。还可以通过测序（“测序分析”）生成“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以及哪些基因编码调节RNA。它还可以告诉我们 DNA 序列中负责基因开启或关闭的其他特征，例如在特定组织中或响应信号分子。因此，功能序列数据非常重要，它可以让我们了解个体 DNA 序列的差异如何影响基因活性，从而可能影响表型，例如生产或抗病性状。一些 DNA 数据库包含养殖动物和伴侣动物的功能数据，通常以原始形式（例如序列读取），但是，当这些数据经过质量检查和进一步处理（例如将其分配给特定基因和转录本）时，这些数据才最有用。如果世界各地的研究界向这些数据库提交更多数据，那就更好了。我们提出的研究旨在查看公共 DNA 数据库中这些动物的可用数据，并检查其质量。我们还将努力确保未来提交到数据库的数据集具有尽可能多的与之相关的有用信息，例如品种、性别和组织类型等。我们还将定义此类数据的质量标准并改进数据通过将不同项目的数据集汇集到一个可通过编程方式和网站访问的有凝聚力的集合中，从而提高可发现性。

项目成果

<strong>From </strong><strong>FAANG</strong> <strong>to</strong> <strong>Fork</strong><strong>: Application of Highly Annotated Genomes </strong><strong>to</strong><strong> Improve Farmed Animal Production</strong>

<strong>从</strong><strong>FAANG</strong> <strong>到</strong> <strong>Fork</strong><strong>：高度注释基因组的应用</strong><strong>到<

• DOI: 10.20944/preprints202010.0118.v1
• 发表时间: 2020
• 作者: Clark E

Ensembl 2022.

• DOI: 10.1093/nar/gkab1049
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cunningham F;Allen JE;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Austine-Orimoloye O;Azov AG;Barnes I;Bennett R;Berry A;Bhai J;Bignell A;Billis K;Boddu S;Brooks L;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;Donaldson S;El Houdaigui B;El Naboulsi T;Fatima R;Giron CG;Genez T;Martinez JG;Guijarro-Clarke C;Gymer A;Hardy M;Hollis Z;Hourlier T;Hunt T;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Marugán JC;Mohanan S;Mushtaq A;Naven M;Ogeh DN;Parker A;Parton A;Perry M;Piližota I;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Pérez-Silva JG;Stark W;Steed E;Sutinen K;Sukumaran R;Sumathipala D;Suner MM;Szpak M;Thormann A;Tricomi FF;Urbina-Gómez D;Veidenberg A;Walsh TA;Walts B;Willhoft N;Winterbottom A;Wass E;Chakiachvili M;Flint B;Frankish A;Giorgetti S;Haggerty L;Hunt SE;IIsley GR;Loveland JE;Martin FJ;Moore B;Mudge JM;Muffato M;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Dyer S;Harrison PW;Howe KL;Yates AD;Zerbino DR;Flicek P
• 通讯作者: Flicek P

The European Nucleotide Archive in 2020.

• DOI: 10.1093/nar/gkaa1028
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Harrison PW;Ahamed A;Aslam R;Alako BTF;Burgin J;Buso N;Courtot M;Fan J;Gupta D;Haseeb M;Holt S;Ibrahim T;Ivanov E;Jayathilaka S;Balavenkataraman Kadhirvelu V;Kumar M;Lopez R;Kay S;Leinonen R;Liu X;O'Cathail C;Pakseresht A;Park Y;Pesant S;Rahman N;Rajan J;Sokolov A;Vijayaraja S;Waheed Z;Zyoud A;Burdett T;Cochrane G
• 通讯作者: Cochrane G

Ensembl 2021.

• DOI: 10.1093/nar/gkaa942
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
• 通讯作者: Flicek P

The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes.

• DOI: 10.3389/fgene.2021.639238
• 发表时间: 2021
• 期刊: Frontiers in genetics
• 影响因子: 3.7
• 作者: Harrison PW;Sokolov A;Nayak A;Fan J;Zerbino D;Cochrane G;Flicek P
• 通讯作者: Flicek P