A Review of Gene and Isoform Expression Analysis across Multiple Experimental Platforms
Wang Kaili1, Zhang Li2, Liu Xuejun1*
1(College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China) 2(College of Informaiton Science and Technology, Nanjing Forestry University, Nanjing 210037, China)
Abstract：Transcriptomics study has become a hot topic in life science and medical research in recent years. From the expression point of view, the foundation of transcriptomics study is the measurement of gene expression levels. Differential expression (DE) analysis of genes is very important for understanding the function of genes. DE analysis of isoforms is a feasible method to reflect the change of alternative splicing. Currently, there are mainly two large-scale experimental platforms for measuring gene expression levels, including microarray and high-throughput sequencing technology, RNA-Seq. At the beginning of this paper, we introduced the technical principles of the four mainstream experimental platforms: Affymetrix's traditional 3' GeneChip, Exon array, Human Transcriptome Array 2.0 and Illumina platform based on RNA-Seq. We then reviewed the mainstream analysis methods and our methods on each platform for the calculation of gene expression levels and DE analysis. We also showed the comparison results of expression measurement and DE analysis across various platforms under a well-defined benchmark data set.
王凯莉, 张 礼, 刘学军. 多实验平台下基因及异构体表达分析综述[J]. 中国生物医学工程学报, 2017, 36(2): 211-218.
Wang Kaili, Zhang Li, Liu Xuejun. A Review of Gene and Isoform Expression Analysis across Multiple Experimental Platforms. Chinese Journal of Biomedical Engineering, 2017, 36(2): 211-218.
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