Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 Page 5 of 11 Table 4 Top-ranking GO biological process terms for genes DE between high and low marbled muscles Entrez gene accession no Gene Symbol Gene description GO term/Affymetrix probe identifier Gene more highly expressed in high marbled muscle Protein kinase cascade:GO0007243 Bt.21268.1.S2_at 404181 Protein catabolic process:GO0006516 Bt.15675.1.S1_at 286806 Germ cell development:GO0007281 Bt.21268.1.S2_at 404181 Cholesterol biosynthetic process:GO0006695 Bt.621.1.S1_at 505060 Regulation of Rab GTPase activity:GO0032313 Bt.21021.1.S1_at 532704 Gene more highly expressed in low marbled muscle Protein kinase cascade:GO0007243 Bt.21827.2.S1_at 510889 Peptide metabolic process:GO0006518 Bt.21827.2.S1_at 510889 RPS6KB1 ADAMTS4 RPS6KB1 CYP51 TBC1D7 THOP1 THOP1 Ribosomal protein S6 kinase, 70 kDa, polypeptide 1 ADAM metallopeptidase with thrombospondin type 1 motif, 4 Ribosomal protein S6 kinase, 70 kDa, polypeptide 1 Cytochrome P450, family 51, subfamily A polypeptide 1 TBC1 domain family, member 7 Thimet oligopeptidase 1 Thimet oligopeptidase 1 between two muscle types across three breeds. In this study however, fat metabolism related genes such as FABP4, SCD and LPL in muscle with divergent marbling phenotypes in late stage cattle were not detected. A similar study done by Liu et al. [17] in pigs indicated that FABP4 was differentially expressed among muscle samples with a divergent intramuscular fat content at 70 kg but wasn’t different at a later stage (110 kg body weight). These findings suggest that many lipogenic related genes, including FABP4, will be more active during early growth during which IMF deposition is more intense, rather than at later growth stages. Alter- natively, FABP4 is not detected as differentially expressed because all intramuscular fat was removed from the muscle samples used in this study (see details in the methods section). In our study, all 21 differentially expressed genes were validated by real-time PCR. As shown in Figure 2, both methods showed consistent gene expression fold changes between the high and low marbled groups. Figure 3 Pathway studio analysis of 21 differentially expressed genes. Out of 14 annotated genes, 9 genes were found to be involved in direct interactions. Five main pathway “hubs” (SH3KBP1, ADAMTS4, CYP51A THOP1 and SQLE) were detected in this pathway analysis. Each arrow indicates interactions between genes and a cell process pathway.