comparison of computational models for assessing conservation of gene expression across species计算模型的比较来评估保护跨物种的基因表达.pdf

Comparison of Computational Models for Assessing Conservation of Gene Expression across Species 1,2 1 1,2,3 Yupeng Wang *, Kelly R. Robbins , Romdhane Rekaya 1 Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America, 2 Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America, 3 Department of Statistics, University of Georgia, Athens, Georgia, United States of America Abstract Assessing conservation/divergence of gene expression across species is important for the understanding of gene regulation evolution. Although advances in microarray technology have provided massive high-dimensional gene expression data, the analysis of such data is still challenging. To date, assessing cross-species conservation of gene expression using microarray data has been mainly based on comparison of expression patterns across corresponding tissues, or comparison of co- expression of a gene with a reference set of genes. Because direct and reliable high-throughput experimental data on conservation of gene expression are often unavailable, the assessment of these two computational models is very challenging and has not been reported yet. In this study, we compared one corresponding tissue based method and three co-expression based methods for assessing conservation of gene expression, in terms of their pair-wise agreements, using a frequently used human-mouse tissue expression dataset. We find that 1) the co-expression based methods are only moderately correlated with the corresponding tissue based methods, 2) the reliability of co-expression based methods is affected by the size of the reference ortholog set, and 3)