ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange

ProteoGenomics：通过 Ensembl 和 ProteomeXchange 动态链接基因组和蛋白质组

• 批准号: BB/L024225/1
• 负责人: Henning Hermjakob
• 金额: $ 61.39万
• 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: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL024225%2F1
• 关键词: ProteoGenomics; Dynamic; Linkage; Genomes; Proteomes

For researchers in the Life Sciences, it imperative that they are able to access and view the human genome, and genomes of model organisms and human pathogens in an efficient and user-friendly way via the Internet. The genome itself is annotated with information about the locations and functions of genes, and quantitative data about genes and other elements within the genome. The UK-based Ensembl project is a leading genome browser, used by thousands of researchers every day. The value of genomic information is greatly increased when it is integrated with and can be directly viewed alongside other biological data sources such as proteomics - a set of technologies devoted to the identification and quantification of proteins, the functional molecules encoded by each gene. From a technical point of view, the large size of modern biological data sets makes it challenging to efficiently integrate them into genome browsers. A technology called DAS (Distributed Annotation System) is the prevalent technology used by genome browsers to integrate external data but it can no longer support much-needed new features or scale to the sizes of modern data sets. Another genome browser, the UCSC Genome Browser, has developed a more modern and efficient technology, specifically designed for large-scale data sets called 'TrackHubs'. Both UCSC and Ensembl have developed initial support for this technology, but there are still limitations for many users, and Ensembl's support remains incomplete. In the 'ProteoGenomics' project, we first want to further develop the 'TrackHub' technology, expanding its scope of usage in Ensembl, and making it easier for researchers around the world to discover and use TrackHubs containing different types of research data. Ensembl's TrackHub technology will be expanded to proteomics data for the first time and thus improve the provision of non-genomics biological information in this widely used resource.In the project, we are going to build technology to integrate proteomics data with the genome data held in Ensembl, in a dynamic and effective way. With this aim in mind we will use public MS proteomics data submitted and available in one of the main repositories in the world, the UK-based resource PRIDE, which is also one leading the ProteomeXchange Consortium of proteomics resources. We will reanalyse the data in PRIDE via our ProteoAnnotator pipeline to provide updated or complementary information to the results originally submitted by the research team that generated the data. We are pioneering techniques for extracting more value from the same data, to understand how proteins vary in their abundance and in chemical modifications that occur on proteins, altering their function, two types of results often not generated initially by research groups submitting data to PRIDE. Through this data reuse and the extraction of new biological findings, the value of the submitted datasets will increase. In addition, 'ProteoGenomics' will provide a portal for datasets from the recently started Human Proteome Project (HPP), providing the global research community with a single entry point to these datasets.

对于生命科学的研究人员来说，他们必须能够通过互联网以有效和用户友好的方式访问和查看人类基因组以及模式生物和人类病原体的基因组。基因组本身被注释了基因的位置和功能的信息，以及基因组内基因和其他元素的定量数据。总部位于英国的Ensembl项目是一个领先的基因组浏览器，每天有数千名研究人员使用。当基因组信息与其他生物数据源（如蛋白质组学-一套专门用于鉴定和定量蛋白质（每个基因编码的功能分子）的技术）相结合并可直接查看时，其价值将大大增加。从技术角度来看，现代生物数据集的庞大规模使得将其有效整合到基因组浏览器中具有挑战性。一种名为DAS（分布式注释系统）的技术是基因组浏览器用于集成外部数据的流行技术，但它不再支持急需的新功能或扩展到现代数据集的大小。另一个基因组浏览器，UCSC基因组浏览器，开发了一种更现代和更有效的技术，专门为大规模数据集设计，称为“TrackHub”。UCSC和Ensembl都已经开发了对这项技术的初步支持，但对许多用户来说仍然存在限制，Ensembl的支持仍然不完整。在“ProteoGenomics”项目中，我们首先希望进一步开发“TrackHub”技术，扩大其在Ensembl的使用范围，并使世界各地的研究人员更容易发现和使用包含不同类型研究数据的TrackHub。Ensembl的TrackHub技术将首次扩展到蛋白质组学数据，从而改善在这一广泛使用的资源中提供非基因组学生物信息的情况。在该项目中，我们将构建技术，以动态有效的方式将蛋白质组学数据与Ensembl保存的基因组数据整合在一起。考虑到这一目标，我们将使用在世界上主要的资源库之一，英国的资源PRIDE中提交和提供的公共MS蛋白质组学数据，这也是蛋白质组学资源ProteomeXchange联盟的领导者之一。我们将通过我们的ProteoAnnotator管道重新分析PRIDE中的数据，为生成数据的研究团队最初提交的结果提供更新或补充信息。我们正在开拓技术，从相同的数据中提取更多的价值，了解蛋白质在其丰度和蛋白质上发生的化学修饰中如何变化，改变它们的功能，这两种类型的结果通常不是由向PRIDE提交数据的研究小组最初产生的。通过这种数据再利用和提取新的生物学发现，提交的数据集的价值将增加。此外，“ProteoGenomics”将为最近启动的人类蛋白质组计划（HPP）的数据集提供一个门户，为全球研究界提供这些数据集的单一入口点。

项目成果

Ensembl 2015.

• DOI: 10.1093/nar/gku1010
• 发表时间: 2015-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cunningham F;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Johnson N;Juettemann T;Kähäri AK;Keenan S;Martin FJ;Maurel T;McLaren W;Murphy DN;Nag R;Overduin B;Parker A;Patricio M;Perry E;Pignatelli M;Riat HS;Sheppard D;Taylor K;Thormann A;Vullo A;Wilder SP;Zadissa A;Aken BL;Birney E;Harrow J;Kinsella R;Muffato M;Ruffier M;Searle SM;Spudich G;Trevanion SJ;Yates A;Zerbino DR;Flicek P
• 通讯作者: Flicek P

Ensembl 2017.

• DOI: 10.1093/nar/gkw1104
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Aken BL;Achuthan P;Akanni W;Amode MR;Bernsdorff F;Bhai J;Billis K;Carvalho-Silva D;Cummins C;Clapham P;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Juettemann T;Keenan S;Laird MR;Lavidas I;Maurel T;McLaren W;Moore B;Murphy DN;Nag R;Newman V;Nuhn M;Ong CK;Parker A;Patricio M;Riat HS;Sheppard D;Sparrow H;Taylor K;Thormann A;Vullo A;Walts B;Wilder SP;Zadissa A;Kostadima M;Martin FJ;Muffato M;Perry E;Ruffier M;Staines DM;Trevanion SJ;Cunningham F;Yates A;Zerbino DR;Flicek P
• 通讯作者: Flicek P

The ProteomeXchange consortium at 10 years: 2023 update.

• DOI: 10.1093/nar/gkac1040
• 发表时间: 2023-01-06
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Deutsch, Eric W.;Bandeira, Nuno;Perez-Riverol, Yasset;Sharma, Vagisha;Carver, Jeremy J.;Mendoza, Luis;Kundu, Deepti J.;Wang, Shengbo;Bandla, Chakradhar;Kamatchinathan, Selvakumar;Hewapathirana, Suresh;Pullman, Benjamin S.;Wertz, Julie;Sun, Zhi;Kawano, Shin;Okuda, Shujiro;Watanabe, Yu;MacLean, Brendan;MacCoss, Michael J.;Zhu, Yunping;Ishihama, Yasushi;Vizcaino, Juan Antonio
• 通讯作者: Vizcaino, Juan Antonio

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

• DOI: 10.1021/acs.jproteome.7b00370
• 发表时间: 2017-12-01
• 期刊: Journal of proteome research
• 影响因子: 4.4
• 作者: Deutsch EW;Orchard S;Binz PA;Bittremieux W;Eisenacher M;Hermjakob H;Kawano S;Lam H;Mayer G;Menschaert G;Perez-Riverol Y;Salek RM;Tabb DL;Tenzer S;Vizcaíno JA;Walzer M;Jones AR
• 通讯作者: Jones AR

Improving the Sequence Ontology terminology for genomic variant annotation.

• DOI: 10.1186/s13326-015-0030-4
• 发表时间: 2015
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Cunningham F;Moore B;Ruiz-Schultz N;Ritchie GR;Eilbeck K
• 通讯作者: Eilbeck K