Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 Table 3 GO Biological processes significantly altered following infection GO Identifier1 Term2 Immune related GO:0006952 GO:0009611 GO:0006954 GO:0002526 Protein metabolism GO:0006519 GO:0009308 GO:0044106 GO:0006520 Energy metabolism GO:0019752 GO:0005975 GO:0044262 GO:0019318 Catabolic process GO:0044282 GO:0046164 GO:0046395 GO:0009063 Other Processes GO:0044281 GO:0043436 GO:0040011 GO:0030003 defense response response to wounding inflammatory response acute inflammatory response cellular amino acid and derivative metabolic process amine metabolic process cellular amine metabolic process cellular amino acid metabolic process carboxylic acid metabolic process carbohydrate metabolic process cellular carbohydrate metabolic process hexose metabolic process small molecule catabolic process alcohol catabolic process carboxylic acid catabolic process cellular amino acid catabolic process small molecule metabolic process oxoacid metabolic process locomotion cellular cation homeostasis q3 30 27 25 19 64 55 53 51 80 52 42 33 43 23 21 19 12 3 4 137 80 20 15 m4 110 102 70 39 296 284 256 253 372 244 193 138 173 96 82 70 33 5 7 683 372 53 50 Page 8 of 20 p5 0.00 0.01 0.00 0.00 0.00 0.09 0.02 0.05 0.00 0.01 0.03 0.02 0.00 0.09 0.05 0.04 0.01 0.08 0.04 0.00 0.00 0.00 0.04 Lipid and steroid metabolism GO:0006720 isoprenoid metabolic process GO:0045444 fat cell differentiation GO:0006775 fat-soluble vitamin metabolic process Gene ontology (GO) identifiers significantly over represented in genes differentially expressed following infection. In total 698 regulated (414 up regulated and 284 down regulated) genes were included in the list for GO analysis. 1Gene ontology identifier, 2Gene Ontology term, 3number of times the GO term is present in the gene list, 4number of times the GO term is present on the filtered array list, 5statistical enrichment for GO term. Only GO terms that appear 3 or more times are shown. Full list is shown in Additional file Table S2. these being concerned with metabolism of specific amino acids rather that synthesis and turnover of pro- teins. Genes related to energy metabolism via glycolysis were also down regulated following infection, as well as genes encoding enzymes in gluconeogenic pathways, perhaps reflecting a reduced use of amino acids as an energy source. Lipid and steroid metabolism There was a general decrease in genes related to lipid and steroid metabolism in those fish that were infected, specifically peroxisomal enzymes and a fatty acid desaturase. A nuclear peroxisome prolifera- tor-activated receptor, a critical regulator of the cholesterol and inflammatory response in macro- phages, was increased following infection suggesting tight control of cholesterol metabolism in the infected animals. This can explain the increase in steroid bio- genesis related genes including isopentenyl pyropho- sphate isomerise 1 and steroidogenic acute regulatory factor that were increased following infection, so as to maintain correct cholesterol balance and potential pro- duction of prostaglandins. The genes related to trans- port of lipids, apolipoprotein (Apo) B, Apo A-I and Apo H were decreased in expression following disease in the ASL group, proteins highly abundant in the plasma. Another plasma protein, serum albumin, was