Abstract
BackgroundIt is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. However, the level of conservation of gene expression patterns of the orthologous genes in different species has been unclear. To address the issue, we compared gene expression of orthologous genes based on 2,557 human and 1,267 mouse samples with high quality gene expression data, selected from experiments stored in the public microarray repository ArrayExpress.ResultsIn a principal component analysis (PCA) of combined data from human and mouse samples merged on orthologous probesets, samples largely form distinctive clusters based on their tissue sources when projected onto the top principal components. The most prominent groups are the nervous system, muscle/heart tissues, liver and cell lines. Despite the great differences in sample characteristics and experiment conditions, the overall patterns of these prominent clusters are strikingly similar for human and mouse. We further analyzed data for each tissue separately and found that the most variable genes in each tissue are highly enriched with human-mouse tissue-specific orthologs and the least variable genes in each tissue are enriched with human-mouse housekeeping orthologs.ConclusionsThe results indicate that the global patterns of tissue-specific expression of orthologous genes are conserved in human and mouse. The expression of groups of orthologous genes co-varies in the two species, both for the most variable genes and the most ubiquitously expressed genes.
Highlights
It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms
Sample clustering analysis of the mouse dataset An integrated mouse gene expression dataset based on Affymetrix platform MG_U74Av2 was created as described in Materials and methods. It can be downloaded from the ArrayExpress website [26], accession number E-MTAB-27
To explore whether the 1,323 samples form distinct groups based on their gene expression profiles, the data matrix was subjected to principal component analysis (PCA) and the results are visualized by scatter plots
Summary
It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. Some studies used the same microarray for cross-hybridization in samples from different species to eliminate the variations in hybridization and scanning protocols This approach typically used either a singlespecies array, to which samples from closely related species or subspecies were hybridized and expression levels of orthologous genes were measured [12,13], or a custom-designed chip that contained probes from different species [14,15]. Many other studies made use of species-specific arrays to identify coexpressed groups of orthologous genes [4,5,6,16,17] In such studies, how to minimize the platform effects was the key to meaningful comparison of the cross-species data. A few other studies used more sophisticated algorithms and analyzed combined data from different species at the same time to identify cell cycle genes with conserved expression patterns between species [19,20,21]
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