PMC4277429_01
Differentially expressed genes between males and females in a population of Nigerian individuals.. (A) Significant detections identified with gene-based or exon-based limma at FDR<0.05, an absolute fold change of at least 1.5 and at least 5 exons. With the exon-based strategy, we additionally required that the median p-value was below 0.05. Notably, all the gene-based detections were also found using the exon-based strategy, while the list of exon-based detections missed by the gene-based strategy contains 51 genes (B) The 67 genes detected using the exon-based approach with limma; genes reported as sex-specific in earlier studies or belonging to chromosome Y are shown on the left side. Genes detected also with the gene-based approach are highlighted with grey background. Red background in the chromosome column denotes higher expression in male than in female, blue vice versa. (C) Two examples of genes on the X chromosome that have previously been reported as sex-specific but were detected here only with the exon-based strategy. Both genes show moderate but systematic changes across the exons (x-axis). The number of stars above a bar indicates if only one or both of the two software packages (limma and edgeR) identify the particular exon as significant at p<0.05. The fold changes (female vs. male) were determined using the limma software package.
pone.0115964.g004.jpg
PMC4277429_01_pone.0115964.g004.jpg
pone-0115964-g004
Focusing only on the most promising genes identified at FDR<0.05 and showing at least a 1.5-fold change between the male and female groups across at least five exons, we identified 16 and 67 genes using limma with the gene- and exon-based strategies, respectively (Fig. 4A and B). All of the gene-based detections were among the exon-based detections (highlighted in grey in Fig. 4B). Fig. 4C illustrates two such example genes from the X chromosome that have previously been reported as sex-specific but were detected here only with the exon-based strategy. A systematic comparison of the detections to the previously reported sex-specific genes on the X chromosome and genes on the Y chromosome also revealed a high overlap as shown in Fig. 4B (left panel).