Computational framework for analysis of microarray gene expression data

描述（由申请人提供）：鉴定在所研究的实验条件下差异调节的转录本是DNA微阵列数据分析的关键步骤之一。目前采用的统计方法对于在差异表达研究中普遍存在的具有少量生物重复的实验变得特别无效。我们建议开发和验证一种新的数值框架，用于识别差异表达的转录本，重点是分析少量重复和中等水平表达的基因的实验。所提出的方法是基于一种新的，非参数的方法来评估微阵列数据中的噪声分布，这是直接从分析的数据集。将实施三种不同的单变量和多变量方法来鉴定差异表达的基因，并将其结果与领先的先进统计方法的结果进行比较。在I期可行性研究中，我们将分析大鼠和小鼠中至少9种具有不同相似性水平的正常组织之间的差异基因表达。将使用来自SymAtlas数据库（诺华研究基金会基因组学研究所）的公开可用数据，这些数据是通过Affyssin微阵列获得的。新开发的数值方法的实用性将通过使用功能分析（如果功能注释可用）和/或定量聚合酶链反应分析对已识别的基因组生物标志物进行生物学和/或实验验证来建立。公共卫生相关性：DNA微阵列技术能够同时分析在特定生物体、细胞或组织中表达的数千种转录物。其目前的应用包括基因分析、基因调控研究、疾病生物标志物发现、毒理基因组学、药物基因组学以及临床诊断和预后。尽管最近令人印象深刻的技术进步，主要的瓶颈，实现的全部潜力的微阵列技术存在，包括不完整的功能基因注释和缺乏有效的计算数据分析工具。本项目开发的分析方法将提高在具有少量生物重复的实验中可靠地鉴定差异表达基因的能力，这将提高该技术的整体有效性并降低微阵列基因表达研究的成本。

DESCRIPTION (provided by applicant): Identification of transcripts that are differentially regulated in response to studied experimental conditions is one of critical steps in analysis of DNA microarray data. Currently employed statistical approaches become particularly ineffective for experiments with small number of biological replicates, which are prevalent in the differential expression studies. We propose to develop and validate a novel numerical framework for identification of differentially expressed transcripts, with emphasis on analysis of experiments with small number of replicates and genes with moderate levels of expression. The proposed approach is based on a novel, non-parametric method for assessment of noise distributions in microarray data, which are derived directly from the analyzed data set. Three distinct, univariate and multivariate methods for identification of differentially expressed genes will be implemented and their results will be compared to the results of leading advanced statistical methods. In the Phase I feasibility study we will analyze differential gene expression between at least nine normal tissues with varying levels of similarity, in rat and mouse. Publicly available data from SymAtlas database (Genomics Institute of the Novartis Research Foundation), obtained with Affymetrix microarrays, will be employed. The utility of newly developed numerical methods will be established through biological and/or experimental validation of identified genomic biomarkers using functional analysis (if functional annotation is available) and/or quantitative polymerase chain reaction analysis. PUBLIC HEALTH RELEVANCE: DNA microarray technology enables simultaneous profiling of thousands of transcripts expressed in particular organism, cells or tissues. Its current applications include gene profiling, gene regulation studies, disease biomarker discovery, toxicogenomics, pharmacogenomics, and clinical diagnostics and prognosis. Despite recent impressive technological advances, major bottlenecks to the realization of the full potential of the microarray technology exist and include incomplete functional gene annotation and the lack of effective computational data analysis tools. The analysis methods developed in this project will improve the ability to reliably identify differentially expressed genes in experiments with small number of biological replicates, which will improve the overall effectiveness of this technology and reduce the cost of microarray gene expression studies.