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Recently, several statistical methods have been independently proposed for estimating the degree (n) of gene pleiotropy (i.e. the capacity of a gene to affect many phenotypes) without knowing measurable phenotypic traits. However, the theoretical limitation of these approaches has not been well demonstrated. In this short note, we show that our previous method based on the phylogeny of protein sequences is, in fact, an effective estimate of a parameter that can be written symbolically as K = min(n,r), where r is the rank of mutations at an amino acid site. Hence, understanding of r is crucial for appropriate interpretation of the estimated K, denoted by Ke (the effective gene pleiotropy). Indeed, when protein sequence alignment is used to estimate effective gene pleiotropy (Ke) by this method, Ke can be interpreted as an effective estimate of n when n ≤ 20, as long as the phylogeny is sufficiently large. If n > 20, Ke 20, although the true n could be much higher.

To study the expression profiles in the heart tissues of domestic pigs,five un-normalized cDNA libraries from Danish adult female Landrace heart, biceps femoris, aorta, left ventricle tissues and Chinese adult female Erhualian heart tissue were constructed. Totally 35 180 expressed sequence tags (ESTs) were randomly sequenced. Using functional clustering and statistic methods, three gene clusters and 47 genes highly expressed in Landrace heart tissue were found. These genes are corresponding to the chaperone activity, motor activity and physiology process, implying the functional importance of the protection and movement process in heart. Between the two pig breeds, most of the differentially expressed genes are related with energy metabolism and catalytic activity, of which the majority are highly expressed in Landrace. The results indicate that the physiological activities of Landrace heart are more active and effective than Erhualian heart.