CLIP Tool Kit (CTK): pipeline, user interface and tutorials for CLIP data analysis

CLIP 工具套件 (CTK)：用于 CLIP 数据分析的管道、用户界面和教程

• 批准号: 9294442
• 负责人: Chaolin Zhang
• 金额: $ 8万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-10 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9294442
• 关键词: Algorithms; Biochemical; Bioinformatics; Biological Assay; Biology; Biotechnology; Code; Communities; Complex; Computer software; Custom; Data; Data Analyses; Dependency; Development; Disease; Feedback; Galaxy; Gene Expression Regulation; Genetic Transcription; Genome; Genomics; Gold; Hereditary Disease; High-Throughput Nucleotide Sequencing; Immunoprecipitation; Individual; Induced Mutation; Libraries; Maintenance; Malignant Neoplasms; Maps; Modeling; Names; Nature; Noise; Nucleotides; Online Systems; Output; Play; Post-Transcriptional RNA Processing; Process; Proteins; Protocols documentation; Publishing; RNA; RNA-Binding Proteins; RNA-Protein Interaction; Regulation; Research; Research Personnel; Resolution; Resources; Role; Series; Signal Transduction; Site; Software Engineering; Software Tools; Statistical Methods; System; Technology; Variant; base; crosslink; experience; experimental study; flexibility; genome-wide; improved; in vivo; mammalian genome; nervous system disorder; novel; prototype; tool; usability

Project summary CLIP Tool Kit (CTK): software package, user interface and tutorials for CLIP data analysis Multiple steps of gene expression regulation rely on co- and post-transcriptional processing of RNA through its interaction with RNA-binding proteins (RBPs). UV cross-linking and immunoprecipitation (CLIP) of protein- RNA complexes, followed by high-throughput sequencing of isolated RNA, has become a gold standard for mapping in vivo protein-RNA interactions on a genome-wide scale. However, there remains a lack of software tools that provide flexible, streamlined and comprehensive analysis of CLIP data that incorporates the most recent technical advancements of CLIP protocols and sequencing technology. Here we propose to develop the CLIP Tool Kit (CTK) to fill this gap by building on our extensive experience in this field and enhancing a prototype we have developed for our research over the years. Taking raw sequence reads coming off sequencers as input, CTK will perform a series of analyses using its three major components: 1) quality filtering and mapping of raw reads, followed by a stringent, model-based algorithm to collapse PCR duplicates to obtain unique CLIP tags; 2) an adaptive valley-seeking algorithm to define CLIP tag clusters and perform peak calling; and 3) a statistical method to determine the exact protein-RNA crosslink sites through analysis of crosslink induced mutation sites (CIMS) and truncation sites (CITS). We will implement several novel algorithms as well as important extensions to our current software package, to make significant improvement in accuracy and efficiency, and to keep up with advancement in CLIP protocols and sequencing technologies. In addition, we aim to improve the usability and dissemination of the software. We will implement an interface through Galaxy so that CTK can be integrated into this widely used bioinformatics workflow management system. Multiple tutorials for typical analysis pipelines will be developed and a user group will be established. Thus, this study will provide a valuable resource for the RNA biology research community.

项目总结 CLIP工具包(CTK)：CLIP数据分析的软件包、用户界面和教程 基因表达调控的多个步骤依赖于通过ITS对RNA进行共转录和转录后处理 与RNA结合蛋白(RBPs)的相互作用。蛋白质的紫外光交联和免疫沉淀(CLIP) RNA复合体，然后是分离的RNA的高通量测序，已经成为 在全基因组范围内绘制体内蛋白质-RNA相互作用图。然而，仍然缺乏软件 提供灵活、简化和全面的剪辑数据分析工具，该工具结合了 CLIP协议和测序技术的最新技术进展。在这里，我们建议开发 Clip Tool Kit(CTK)以我们在该领域的丰富经验为基础，增强了 多年来，我们为我们的研究开发了原型。正在进行原始序列读取 作为输入，CTK将使用其三个主要组件执行一系列分析：1)质量 对原始读取进行过滤和映射，然后使用严格的、基于模型的算法来折叠PCR副本 2)自适应寻谷算法定义片段标签簇并执行 高峰呼叫；以及3)通过对蛋白质-RNA交联点的分析来确定准确的蛋白质-RNA交联点的统计方法 交链诱导突变位点(CIMS)和截断位点(CITS)。我们将实施几部小说 算法以及对我们当前软件包的重要扩展，以在 准确性和效率，并跟上剪辑协议和测序技术的进步。在……里面 此外，我们的目标是提高软件的可用性和传播性。我们将实现一个接口 通过Galaxy使CTK可以集成到这个广泛使用的生物信息学工作流管理中 系统。将为典型分析管道开发多个教程，并将建立一个用户组。 因此，这项研究将为RNA生物学研究界提供有价值的资源。