Bioinformatics and Biostatistics Core

生物信息学和生物统计学核心（BBC）：项目摘要 1.我们的生物信息学工作将通过以下方式支持中心的总体目标。 a）整合蛋白质组学、转录组学和基因组学数据，以允许异构体水平的询问， 蛋白质组 B）提供啮齿动物中mRNA和蛋白质丰度的以同种型为中心的数据库，并扩展到非哺乳动物。 人类灵长类动物和人类物种。 c）通过开发多层次的数据库，整合个体、条件和物种的数据。 网络分析，以补充途径一级的分析。 2.拟议的生物统计工作包括以下组成部分。 a）为当前和未来的实验设计、样品质量评估提供统计学指导， 探索性分析和可视化蛋白质组学数据，包括无标记、多反应 监控和数据独立采集。 B）为MS/蛋白质组学数据开发下游统计分析框架， 差异表达蛋白或肽的标准化和显著性分析。 c）与YPED团队合作，构建基于网络的自动化分析管道。 3.我们将对耶鲁蛋白质表达数据库（YPED）进行以下改进。 a）将新型蛋白质组学数据和相关数据分析纳入网络界面。 B）与生物信息学和生物统计学团队合作，以纳入获得的新数据结果 使用LC-MRM、SWATH和RNA-Seq的新分析管道。 c）通过与神经科学信息框架（NIF）的互操作将YPED链接到外部数据源。 使用NIF本体标准化YPED数据注释并促进与RNA-seq数据的集成。 （d）扩大“青年发展数据库”（“青年发展数据库”的公开部分），以便更迅速地发放更广泛的 向科学界提供各种类型的蛋白质组学数据。 4.高性能计算（HPC）资源提供以下支持。 a）提供大规模肽序列比对的持续支持，并支持新的管道， 整合基因组、转录组和蛋白质组数据集。 B）与数据库、生物信息学和生物统计学团队密切合作，帮助制定基准、规模， 优化和加速涉及大规模MS数据的计算任务。 c）开发开源蛋白质组学管道（例如，Skyline）。 5.研究生和博士后研究员的培训和教育。

Bioinformatics and Biostatistics Core (BBC): Project Summary 1. Our bioinformatics effort will support the overall goals of the Center via the following. a) Integrate proteomic, transcriptomic, and genomic data to allow isoform-level interrogation of the proteome. b) Provide an isoform-centric database of mRNA and protein abundance in rodent, and extend to non- human primate, and human species. c) Integrate data across individuals, conditions, and species through the development of multi-level network analyses to complement pathway-level analyses. 2. The proposed biostatistics efforts include the following components. a) Provide statistical guide for current and future experimental design, sample quality assessment, exploratory analysis, and visualization for proteomics data including label-free, multiple reaction monitoring, and data-independent acquisition. b) Develop a downstream statistical analysis framework for MS/proteomics data that includes data normalization and significance analysis of differentially expressed proteins or peptides. c) Construct an automated web-based analysis pipeline in collaboration with the YPED team. 3. We will make the following improvements to the Yale Protein Expression Database (YPED). a) Incorporate into the web interface new types of proteomics data and associated data analyses. b) Collaborate with the Bioinformatics and Biostatistics teams to incorporate new data results obtained using their new analysis pipelines for LC-MRM, SWATH and RNA-Seq. c) Link YPED to external data sources via interoperation with Neuroscience Information Framework (NIF). Use NIF ontologies to standardize YPED data annotation and facilitate integration with RNA-seq data. d) Expand the YPED repository (the public portion of YPED) to enable more rapid dissemination of a wider variety of types of proteomics data to the scientific community. 4. The high performance computing (HPC) resource provides the following support. a) Provide continued support of large-scale peptide sequence alignment and support novel pipelines to integrate genomic, transcriptomic, and proteomic datasets. b) Work closely with the database, bioinformatics, and biostatistics teams to help benchmark, scale, optimize, and speed up computing tasks involving large-scale MS data. c) Develop open-source proteomics pipelines (e.g., Skyline) in HPC settings. 5. Training and Education of Graduate students and Postdoctoral Fellows.