Global functional profiling of gene expression
Global functional profiling of gene expression
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DOI：
10.1016/s0888-7543(02)00021-6
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发表时间：
2003-02-01
期刊：
影响因子：
4.4
通讯作者：
Krawetz, SA
中科院分区：
文献类型：
--
作者：
Draghici, S;Khatri, P;Krawetz, SA
微阵列实验的典型结果是在所研究的条件下发现的数十或数百个差异调节的基因的列表。与选择这些基因的方法无关，任何研究人员面临的共同任务是将这些基因列表转化为对所涉及的生物现象的更好理解。目前，这是通过一个繁琐的组合搜索通过文献和一些公共数据库。我们开发了Onto-Express（OE）作为一种新的工具，能够自动将这些差异调节基因的列表翻译成功能谱，以表征所研究的条件的影响。OE构建了以下类别的功能图谱（使用基因本体论术语）：生化功能，生物过程，细胞作用，细胞组分，分子功能和染色体位置。计算每个类别的统计学显著性值。我们通过分析来自两个不同实验室的两个乳腺癌数据集，证明了这种全面的全球基因功能分析的有效性和实用性。OE能够正确识别原作者假设的所有生物过程，并发现新的相关机制。(C)2003 Elsevier Science（美国）。All rights reserved.
The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independent of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function, and chromosome location. Statistical significance values are calculated for each category. We demonstrate the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer datasets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms. (C) 2003 Elsevier Science (USA). All rights reserved.