Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 Table 2 GO Biological processes significantly altered following starvation Term2 q3 m4 p5 GO Identifier1 Blood and oxygen transport GO:0015669 gas transport GO:0015671 oxygen transport Amino acid metabolism GO:0006544 glycine metabolic process GO:0006541 glutamine metabolic process Fatty acid and steroid metabolism GO:0006720 isoprenoid metabolic process GO:0016125 sterol metabolic process GO:0008299 isoprenoid biosynthetic process GO:0008203 cholesterol metabolic process Immune function GO:0006953 acute-phase response GO:0009617 response to bacterium GO:0042742 defense response to bacterium GO:0006935 chemotaxis Cellular homeostasis GO:0006873 cellular ion homeostasis GO:0030003 cellular cation homeostasis GO:0048878 chemical homeostasis GO:0050801 ion homeostasis Cellular responses GO:0042221 response to chemical stimulus GO:0009605 response to external stimulus GO:0040011 locomotion GO:0007610 behaviour Other processes GO:0022603 regulation of anatomical structure morphogenesis GO:0001501 skeletal system development GO:0018904 organic ether metabolic process GO:0030334 regulation of cell migration 10 19 0.00 10 19 0.00 5 33 0.05 3 16 0.08 5 33 0.05 4 18 0.03 4 10 0.00 3 15 0.06 3 17 0.09 3 13 0.05 3 13 0.05 7 27 0.00 7 60 0.06 7 50 0.03 7 69 0.09 7 61 0.06 17 184 0.01 10 56 0.00 8 53 0.01 7 37 0.00 4 27 0.08 4 22 0.05 3 8 0.01 3 17 0.09 Gene ontology (GO) identifiers over represented in genes found differentially expressed following infection. In total 175 genes (69 up regulated and 106 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 4 or more times are shown. Full list is shown in Additional file Table S2. Transcriptome changes following infection A large diverse group of genes were found to be modu- lated by the bacterial challenge, with 615 genes increased and 458 decreased with greater than a two fold change. For those genes increased in expression 318 were commonly up regulated in fish fed or starved Page 7 of 20 prior to the infection, whereas 145 and 123 genes were increased uniquely for fish fed prior to infection (AFL) or starved prior to infection (ASL) respectively (Fig. 2). It is of note that there were more than twice as many genes down regulated in ASL with 397 decreased com- pared to 170 in the AFL group, which may reflect he requirement of the starved fish to further down regulate genes in order to mount an adequate immune response. Key genes found modulated are presented in Additional file 3 Table S3. To determine the major biological pro- cesses being altered by the bacterial infection, enrichment for GO identifiers were assigned to 76 significantly enriched biological processes that were altered following the infection (Table 3, Additional file 2 Table S2). The bio- logical processes that were enriched could be grouped to immune related, cellular homeostasis, protein, lipid and energy metabolism and catabolism. Immune related genes As predicted, a large number of genes responding to the bacterial infection could be directly related to immune responses, with GO biological process showing acute phase response proteins, inflammatory response and chemotaxis being significantly up regulated. A number of highly induced genes were acute phase response pro- teins, including serum amyloid A, haptoglobin, comple- ment factors and precerebellin like protein. As part of the immune recognition of pathogens a number of cell surface receptors were also induced such as C type lec- tin receptors and Toll like receptors which initiate further signalling to coordinate the immune response. Up regulated transcription factors included Jun B, CAAT enhancer binding proteins a and b, interferon regulatory factor 2 and inhibitor of NF B amongst others. Genes encoding proteins with direct antibacterial activity were also induced; in particular, hepcidin was dramatically up regulated in both ASL and AFL, and lysozyme was also increased but to a lesser level. Protein and amino acid metabolism The dramatic increase in transcriptional and transla- tional activity for the production of acute phase response proteins and other immune related proteins is expected to have major effects on other processes and potentially at the whole animal level. Ribosomal protein encoding genes and protein elongation factors imply an increase in protein synthesis activity, combined with major protein degradation pathways which were also increased including ubiquitin-proteasome, lysosomal (cathepsins) and calpains. Such changes indicate increased protein turnover reflecting the altered protein production in the liver. A number of genes encoding protein chaperones were increased including heat shock proteins 60, 70 and 108, which could be interpreted as a stress response. Several genes related to amino acid cat- abolism were increased following infection, a number of