Wickramasinghe et al. BMC Genomics 2012, 13:45 http://www.biomedcentral.com/1471-2164/13/45 Page 7 of 14 Figure 2 Expression changes in genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway along the course of lactation. Gene symbols are shown in x-axis and the log2 RPKM expression values at 15, 90 and 250 days are shown in the y-axis. All the genes showed highest expression in day 15 and a significant decrease in expression with progression of lactation. STAT5 is the main transcription factor involved in inducing the expression of milk protein genes after hor- monal induction. At least one binding site for STAT5 has been identified in milk protein genes [40]. Two STAT5 genes, STAT5A and STAT5B, are found in bovine, and both these genes showed higher expression in peak lactation MSC where the animals are in positive energy balance, and the milk yield is highest. Increased expression of STAT5A and STA5B in peak lactation may be a compensatory mechanism to maintain the milk pro- tein composition during the rapid increase in milk yield. Lactose is responsible for maintaining the osmotic pressure in milk. It is a unique product in the mammary alveolar cells and is produced by the enzymatic activity of lactose synthase, which is a combination of b-1, 4 galactosyl transferase encoded by B4GALT1 and a-lac- talbumin encoded by LALBA. Both these genes showed higher expression in transition lactation and decreased expression during the course of lactation (Figure 2), and their expression patterns showed a positive correlation with the lactose concentration in milk, which decreases with advanced lactation [41]. Expression of genes encoding enzymes in milk fat metabolism Milk fat metabolism in the mammary gland can be sub- divided into five distinct processes: fatty acid uptake, de novo fatty acid synthesis, fatty acid desaturation, fatty acid esterification and milk fat secretion. All the impor- tant genes involved in these five processes were expressed in MSC and showed changes in their expres- sion pattern along the course of lactation (Figure 3). Lipoprotein lipase (LPL) and very low density lipopro- tein receptor (VLDLR) gene are two important genes involved in the fatty acid uptake pathway by mammary cells. LPL showed higher expression in transition and peak lactation, whereas the expression of VLDLR increased along the course of lactation (Figure 3A). Acetyl-coenzyme A carboxylase alpha (ACACA), the gene encoding the rate limiting enzyme in de novo fatty