Generating and Managing Large Scale Proteogenomic Data for ENCODE Cell Lines

描述（由申请人提供）：第一个人类基因组序列于2001年公布，但8年后的今天，主要问题仍然存在，例如基因组编码了多少基因，以及这些基因中有多少功能产物由于选择性剪接等现象而编码。国家人类基因组研究所（NHGRI）协调了DNA元件百科全书（ENCODE）项目，通过对人类基因组上的功能元件进行全面分类来回答这些问题。该项目的试点阶段详细研究了1%的基因组，揭示了远远超出经典基因模型预测的广泛转录。发现的转录本中有很大一部分的生物学功能尚不清楚。ENCODE项目现在正在扩大规模，以检查整个人类基因组。结果很可能会与试点项目相呼应，揭示大量的转录，其中很大一部分具有无法解释的功能。蛋白质组学技术可以应用于一个称为蛋白质基因组图谱的过程，以确定无数转录本中的哪些编码蛋白质。该方法已被用于揭示新的基因、新的备选剪接变体、新的起始位点和上游开放阅读框（orf）。虽然在开发蛋白质基因组图谱技术方面已经取得了实质性进展，但使用蛋白质基因组学来协助ENCODE项目的一个重大障碍是缺乏与ENCODE转录图谱工作相协调的蛋白质组学数据集。在这里，我们建议直接从转录工作所研究的相同的I层ENCODE细胞系中生成大规模的蛋白质组学数据集，并将结果与转录作图工作相协调，以确定哪些普遍转录本被翻译。我们的具体目标是：1)使用最先进的质谱方法在ENCODE细胞系上产生大规模的蛋白质组学数据集；2)使用我们的数据库技术来存储、管理和使社区可以访问项目的所有结果；3)使用我们的软件管道将结果映射到最新的人类基因组草图，生成UCSC（加州大学圣克鲁斯分校）基因组浏览器跟踪结果。我们相信，这一结果将是对我们的基因组及其编码的功能产物知识的重大进步。

DESCRIPTION (provided by applicant): The first human genome sequence was published in 2001, yet as of now, eight years later, major questions remain, such as how many genes are encoded by the genome, and of those genes, how many functional products are encoded due to phenomena like alternative splicing. The Encyclopedia of DNA Elements (ENCODE) project has been coordinated by National Human Genome Research Institute (NHGRI) to answer these questions by comprehensively classifying functional elements on the human genome. The pilot phase of the project studied 1% of the genome in detail, revealing extensive transcription well beyond that predicted by classical gene models. The biological function of a significant portion of the discovered transcripts is unclear. The ENCODE project is now scaling up to examine the whole human genome. It is likely that results will echo the pilot project, revealing extensive transcription, a significant fraction of which has unexplained function. Proteomic technologies can be applied, in a process called proteogenomic mapping, to determine which of the myriad transcripts encode proteins. This approach has been used to reveal new genes, new alternative splice variants, new start sites, and upstream open reading frames (ORFs). While substantive progress has been made in developing proteogenomic mapping technologies, a significant hurdle in using proteogenomics to assist with the ENCODE project is the lack of proteomic data sets that are coordinated with the ENCODE transcription mapping efforts. Here we propose to generate large-scale proteomic data sets directly from the same tier I ENCODE cell lines studied by the transcription efforts, coordinating the results with the transcription mapping efforts to determine which of the pervasive transcripts are translated. Our specific aims are to: 1) produce large scale proteomic data sets on ENCODE cell lines using the most advanced mass spectrometry methods, 2) use our database technologies to store, manage, and make accessible to the community all results of the project, and 3) use our software pipeline to map the results to the latest human genome drafts, producing a UCSC (University of California Santa Cruz) genome browser track with the results. We believe the result will be a significant advancement in knowledge about our genomes and the functional products they encode. PUBLIC HEALTH RELEVANCE: The human genome is the blueprint for human life and human health, but we do not yet understand its language - the language of genes. The ENCODE project is deciphering that language systematically, and the goal of this proposal is to accelerate that effort by revealing which parts of the blueprint contain instructions to build proteins.