Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 Page 6 of 11 Figure 4 Gene expression analysis of selected genes in ADAMTS4 pathway: (A) gene expression for ADAMTS4 gene in muscle with divergent IMF and protein content. (B) gene expression for three stimulators (IL17, TNFa and TGFb1) of ADAMTS4 protein in muscle with divergent IMF and protein content. (C) Co-expression of ADAMTS4 and TGFb1. Functional annotation of DEGs Gene Ontology analysis and biological pathway searches were used to explore the functional annotation of the dif- ferentially expressed genes. One of the DEGs, CDC like kinase 1(CLK1) showed a negative correlation with increase in IMF content. This gene is part of the cell cycle signaling pathway. Using a rat model, Xiao et al. 2004 found that the CLK gene was also down-regulated with muscle fat during lactation. This might be due to decreasing expression of genes involved in protein synth- esis through the cell cycle signaling pathway during lacta- tion. Another gene encoding a SH3 domainYSC-like 1 was also up-regulated in animals with high IMF content. The Src homology 3 (SH3) domain is a small protein domain of about 60 amino-acid residues which was first identified as a conserved sequence in the non-catalytic part of several cytoplasmic protein tyrosine kinases. The function of the SH3 domain is not well understood. It seems to mediate the assembly of specific protein com- plexes via binding to proline-rich peptides. SH3 domain containing genes, sorbin and SH3 domain containing 1 (SORBS1), which are involved in insulin-stimulated glu- cose uptake [18] have also been reported as up-regulated in muscle of highly marbled Japanese Black Cattle (Wagyu) [19]. Gene Ontology analysis demonstrated that several genes that were more highly expressed in high marbled muscle are involved in protein catabolic and cholesterol biosynthesis processes. This was also reflected in the pathway analysis, which generated five major pathway “hubs” (SH3KBP1, THOP1, ADAMTS4, CYP51A and SQLE) for the genes more highly expressed in high marbled muscle. CYP51A and SQLE protein appear to be involved in steroid biosynthesis and cholesterol meta- bolism. In particular, CYP51A is activated by two tran- scriptional factors, SP1 and SREBP1 in lipid metabolism. More recently, Chen et al. [20] investigated gene expres- sion of the sterol regulatory element binding transcrip- tion factor 1 (SREBP1) in muscle from differing sexes (female and male) and differing genotype within SREBP1