Abstract
BackgroundIn order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue.ResultsFrom the 15982 significantly expressed coding regions that have been assigned to either the autosomes or the Z chromosome (12979 in brain, 13301 in gonad, and 12372 in heart), roughly 18% were significantly sex-biased in any one tissue, though only 4 gene targets were biased in all tissues. The gonad was the most sex-biased tissue, followed by the brain. Sex-biased autosomal genes tended to be expressed at lower levels and in fewer tissues than unbiased gene targets, and autosomal somatic sex-biased genes had more expression noise than similar unbiased genes. Sex-biased genes linked to the Z-chromosome showed reduced expression in females, but not in males, when compared to unbiased Z-linked genes, and sex-biased Z-linked genes were also expressed in fewer tissues than unbiased Z coding regions. Third position GC content, and codon usage bias showed some sex-biased effects, primarily for autosomal genes expressed in the gonad. Finally, there were several over-represented Gene Ontology terms in the sex-biased gene sets.ConclusionOn the whole, this analysis suggests that sex-biased genes have unique genomic and organismal properties that delineate them from genes that are expressed equally in males and females.
Highlights
In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue
Expression properties The genomic distribution of biased and unbiased genes is shown in Table 1, where sex-bias has been denoted by both fold-change and significance parameters
Female-biased genes were more common on the autosomes for both heart and gonad, with autosomal female-biased and male-biased genes being roughly equal for brain
Summary
In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue. Many genes are more actively transcribed in one sex than the other, and this sex-biased expression pattern is a mechanism by which heritable sexual dimorphisms can arise from a genome that is largely identical in males and females [1]. BMC Genomics 2008, 9:148 http://www.biomedcentral.com/1471-2164/9/148 observed in the global transcription profiles of the gonad, which shows the highest degree of sex-biased gene expression of all organs [17,18]. Somatic tissues can exhibit remarkably high sex-biased expression patterns as well [5,17], and these may produce secondary sexual characteristics and behaviors, or result from metabolic differences between males and females
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