Similarly, a total of 391, 313, and 389 strictly sex-biased genes were identified in each strain, respectively. A total of 852, 661, and 826 standard sex-biased genes were identified in B6, CAST, and CD-1 mice, respectively (protein coding and lncRNA genes combined). From left to right, the number of sex-biased genes at the specified threshold is shown for the following groups: PolyA+ RNA-seq from B6 and CAST (this study), and from CD-1 mouse liver, B6 microarray (Jax Strain Survey 26), and CAST microarray (Jax Strain Survey 26 ). The impact of increasing the threshold for sex bias from standard (2-fold) to 4-fold, both at FDR< 0.05, is also shown. Shown is the total number of liver sex-biased protein-coding (PC) genes ( top) and lncRNA genes ( bottom) across B6, CAST, and CD-1 mice. Examples of sex-biased TF genes from S2B Fig, clusters C3 and C5. The three B6-unique sex-biased TFs also show sex-biased expression in CD-1 livers (fold-change > 1.5 and FDR < 0.05).
These genes are putative transcriptional regulators presented in S3 Table. Examples of sex-biased TF genes from S2A Fig, clusters B2, B3 and B4. Three transcriptional regulators that are expressed in a sex-dependent manner, and in the case of Cux2 and Bcl6, have established roles in the regulation of liver sexual dimorphism. No sex-dependence or strain bias is found. Three transcriptional regulators with well-established roles in liver sexual dimorphism (Stat5b, Foxa2, and Hnf4a). Expression data are presented as FPKM values for 6 pooled CD-1 livers (n = 3 per sex), 10 individual B6 livers (n = 5 per sex), and 10 individual CAST livers (n = 5 per sex). S4 Fig: Expression data for TFs related to sex bias that do not show strain-specific expression. In A, clusters B1 and B2 comprise 238 genes that show higher expression in B6 mouse liver and in B, clusters C1 and C2 comprise 142 genes that show higher expression in CAST mouse liver. Hierarchical clustering was performed based on Euclidean distance and is shown to the left of each heat map, with colors indicating the cluster identity labelled to the right of the heat map. Log2 (M/F fold-change) values are shown at the left, with blue indicating male bias and purple indicating female bias for B6 (column marked ’B’) and CAST datasets (column marked ’C’). Expression values are shown as Z-scores normalized per row to visualize patterns independent of the expression level. Heat maps presenting relative expression levels across individual mouse livers (n = 20 5 per sex in each strain) for 301 B6-unique sex-biased protein-coding genes ( A) and for 207 CAST unique sex-biased protein-coding genes ( B), based on data in Sheets C and D in S1 Table. S2 Fig: RNA-seq data for strain-unique sex-biased protein coding genes.
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