Article

Assessing the conservation of mammalian gene expression using high-density exon arrays

Molecular Biology and Evolution (Impact Factor: 14.31). 07/2007; 24(6):1283-5. DOI: 10.1093/molbev/msm061
Source: PubMed

ABSTRACT Microarray data from multiple species have been used to study evolutionary constraints on gene expression. Expression measurements from conventional microarray platforms such as the 3' expression arrays are strongly affected by platform-dependent probe effects that may introduce apparent but misleading discrepancies between species. In this manuscript, we assess the conservation of mammalian gene expression in adult tissues using data from a high-density exon array platform. The exon arrays have more than 6 million probes on a single array targeting all exons in a genome. We find that, unlike 3' array data, gene expression measurements from exon arrays reveal patterns of gene expression that are highly conserved between humans and mice in multiple tissues. Our analysis provides strong evidence for widespread stabilizing selection pressure on transcript abundance during mammalian evolution.

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    • "bp, Figure S3 and Figure S4) are expressed in significantly fewer tissues than SCGI genes are, but in a significantly greater number of tissues than NCGI genes are (Figure 2A, Figure S3, and Figure S4). We observe the same trends using data from exon microarrays (Xing et al. 2007). We use the metric ''tissue specificity index'' for comparing gene expression breadths from exon microarrays (i.e., Liao et al. 2006). "
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    • "The gene expression levels were determined with reference to the data set downloaded from http://biogibbs.stanford.edu/;yxing/MBE/. This data set was generated by examining the transcriptomes of six human tissues (heart, kidney, liver, muscle, spleen, and testis) using a high-density exon array platform (Xing et al. 2007). The expression level of a gene was defined as the average signal intensity across these six examined tissues. "
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