Comparative genomics of gene expression in eukaryotes
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Advances made in genome sequencing in the past decade have produced a massive amount of genetic information. There is a need for developing quantitative methods aimed at exploiting this information, with the ultimate objective being to attain a better understanding of the biological processes taking place. Microarrays, which can characterize the transcriptional profiles of tens of thousands of genes simultaneously, have been widely used in comparative genomic studies. However, the analysis of microarray 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 coexpression of a gene with a reference set of genes. We compared one corresponding tissue-based method and three coexpression-based methods for assessing conservation of gene expression, in terms of their pair-wise agreements, using a frequently used human-mouse tissue expression dataset. Gene expression patterns were then compared between human and mouse genomes using both corresponding tissue-based and coexpression-based methods. To detect and analyze synteny and collinearity, we have developed the MCScanX toolkit, which implements an adjusted MCScan algorithm and incorporates 14 utility programs. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (whole-genome, tandem, proximal, DNA-based transposed, retrotransposed and dispersed duplications), and between positional orthologs. The findings imply that gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.