Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 Page 15 of 20 Isopentyl pyrophosphatase delta isomerase Dimethyl pyrophosphate Acetyl -CoA Hydroxymethyl-Glutaryl-CoA synthetase 3-Hydroxymethyl-Glutaryl-CoA Mevalonate Isopentyl pyrophosphatase Farnesyl pyrophosphate Squalene synthetase Squalene Squalene mono-oxygenase Squalene 2,3,- epoxide Lathosterol Lathosterol oxidase 7-dihydro cholesterol Cholesterol 7-dihydro cholesterol reductase DHEA Bd Bd Bd Plasma lipoproteins & Cholesterol transport Apolipoprotein AI-1 Apolipoprotein B 100 Apolipoprotein H 17 hydroxyl steroid dehydrogenase Steroid hormones Cu1 ACu2 Cu Cu Cu Bd Bd Figure 3 Genes altered in the cholesterol biosynthesis pathway in starved and infected fish. Diagram shows key pathway of cholesterol metabolism. Enzymes circled in blue were found to be differentially expressed during microarray analysis. Those proteins boxed in red are also found altered in expression. 1Cu indicate up regulated in PSL relative to PFL, 2ACu indicates up regulated in AFL and PSL relative to PFL and, 3Bd indicates down regulated in ASL group relative to AFL. Expression levels are shown in supplementary Table S1. both AFL and ASL, indicating increased lipid metabo- lism within the peroxisome. However two enzymes which have activity within the peroxisome were down regulated in the ASL fish, a trans enoyl CoA isomerise and peroxisomal bifunctional enzyme, both involved in fatty acid biosynthesis and metabolism. Potentially the observed changes in lipid metabolism and peroxisomal activity are related to production of eicosanoids, which have a major role in the control of inflammation [74]. Although the precise mechanisms for the reduction in immune gene expression and other biological pathways following starvation are not known, it is likely these are attributable to hormonal factors including glucocorti- coids which are altered following starvation [75] and also have major impacts on the immune system [76]. Conclusions Our transcriptome analysis has demonstrated that star- vation in salmon has profound effects on biological pro- cesses in the liver, with protein, lipid and steroid metabolism being affected. Equally the acute bacterial infection results in a massive increase in APR proteins,