Emig Dorothea, Blankenburg Hagen, Ramírez Fidel, Albrecht Mario
Max Planck Institute for Informatics, Saarbrücken, Germany.
Methods Mol Biol. 2012;910:33-53. doi: 10.1007/978-1-61779-965-5_3.
Complex biological systems comprise a large number of interacting molecules. The identification and detailed characterization of the functions of the involved genes and proteins are crucial for modeling and understanding such systems. To interrogate the various cellular processes, high-throughput techniques such as the Affymetrix Exon Array or RNA interference (RNAi) screens are powerful experimental approaches for functional genomics. However, they typically yield long gene lists that require computational methods to further analyze and functionally annotate the experimental results and to gain more insight into important molecular interactions. Here, we focus on bioinformatics software tools for the functional interpretation of exon expression data to discover alternative splicing events and their impact on gene and protein architecture, molecular networks, and pathways. We additionally demonstrate how to explore large lists of candidate genes as they also result from RNAi screens. In particular, our exemplary application studies show how to analyze the function of human genes that play a major role in human stem cells or viral infections.
复杂的生物系统由大量相互作用的分子组成。对所涉及基因和蛋白质的功能进行鉴定和详细表征，对于构建此类系统的模型和理解该系统至关重要。为了探究各种细胞过程，诸如Affymetrix外显子芯片或RNA干扰（RNAi）筛选等高通量技术是功能基因组学的强大实验方法。然而，它们通常会产生长长的基因列表，这需要计算方法来进一步分析实验结果并进行功能注释，以便更深入地了解重要的分子相互作用。在此，我们专注于用于外显子表达数据功能解读的生物信息学软件工具，以发现可变剪接事件及其对基因和蛋白质结构、分子网络及信号通路的影响。我们还展示了如何探索因RNAi筛选而产生的大量候选基因列表。特别是我们的示例应用研究展示了如何分析在人类干细胞或病毒感染中起主要作用的人类基因的功能。
