Integrative Analysis of Public RNA-seq Repositories

公共 RNA-seq 存储库的综合分析

基本信息

批准号：
8637092
负责人：
XIANGHONG Jasmine ZHOU
金额：
$ 30.89万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-04-01 至 2016-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8637092
关键词：
Address Alternative Splicing Atlases Biological Communities Complex Computer software Computing Methodologies Coupled Coupling Data Data Analyses Data Set Databases Disease Ensure Exons Gene Expression Gene Expression Regulation Genes Genetic Transcription Genomics Graph Human Human Genome Individual Internet Laboratories Lead Ligation Malignant Neoplasms Maps Methods Microarray Analysis Mining Molecular Profiling Mus Ontology Organism Pattern Phenotype Process Production Protein Isoforms Proteins Proteome Protocols documentation RNA Splicing Reader Recurrence Regulation Resolution Resources Sampling Series Side Technology Tissues Transcript Transcriptional Regulation Validation Variant Yeasts base cDNA Library design fly gene function improved insight method development novel open source pressure promoter public health relevance repository software development tissue reconstruction tool transcriptome sequencing

项目摘要

DESCRIPTION (provided by applicant): Recently, the RNA-seq technology is increasingly replacing microarray for expression profiling. In this proposal, we will timely address the emerging challenges and opportunities brought by the rapidly accumulating RNA-seq data. We will design novel methods to perform integrative analysis of many RNA-seq datasets to study the functions and regulations of alternative splicing. In particular, we have the following specifi aims: (1) We will develop a novel graph- based pattern mining method to reconstruct an atlas of splicing modules and identify the associated experimental conditions in human, mouse, fly, and yeast. (2) We will study the coupling between transcription and splicing, the two important regulatory processes, by exploiting both expression and splicing information provided by RNA-seq data. We will design a novel multi-layer network mining approach to systematically identify coupled transcription- splicing modules. (3) We will predict the functions of alternatively spliced transcripts to establish a high-resolution function annotation of human genome. The predicted functions will be incorporated into the GeneOntology and the Ensembl databases to benefit the biological community. (4) We will perform experimental validation on a subset of computational predictions made in Aims 1, 2, 3. (5) We will develop web databases and software to directly benefit the scientific community. Our methods and software will significantly facilitate the re-use of the vast amount of existing RNA-seq data, reduce the necessity to generate new data, and improve our understanding of gene regulations under a variety of perturbations.

描述（由申请人提供）：最近，RNA-seq技术越来越代替微阵列来表达分析。在此提案中，我们将及时解决迅速积累的RNA-Seq数据带来的新出现的挑战和机遇。我们将设计新的方法来对许多RNA-seq数据集进行整合分析，以研究替代剪接的功能和法规。特别是，我们具有以下特定目的：（1）我们将开发一种基于图形的模式挖掘方法来重建剪接模块的地图集，并确定人，小鼠，蝇和酵母中相关的实验条件。（2）我们将通过利用RNA-Seq数据提供的表达和剪接信息来研究转录和剪接之间的耦合，这是两个重要的调节过程。我们将设计一种新型的多层网络挖掘方法，以系统地识别耦合的转录剪接模块。（3）我们将预测剪接的功能转录本以建立人类基因组的高分辨率函数注释。预测的功能将纳入基因生物学和启动数据库中，以使生物群落受益。（4）我们将对目标1，2，3的计算预测的一部分进行实验验证。（5）我们将开发网络数据库和软件，以直接使科学界受益。我们的方法和软件将大大促进重复使用在大量现有的RNA-seq数据中，减少了生成新数据的必要性，并在各种扰动下提高了我们对基因法规的理解。