Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 Page 4 of 11 Table 3 The 21 differentially expressed genes in m. longissimus between high and low marbled Hanwoo Probe ID 1Gene Names 2Fold Change 3P-value (Modified F-test) MAS5.0 RMA GCRMA Mean MAS5.0 RMA GCRMA 1The 21 differentially expressed genes were selected from genes that were significant in at least 2 probe level summarization methods. 2Fold changes are shown on a log2 scale. Positive values show up regulation in high marbled animals and conversely, negative values show down regulation. 3P-value is set to P = 0.01 in this study. Bt.5323.1.S1_at SH3 domain YSC-like 1 (SH3YL1) Bt.15675.1.S1_at ADAM metallopeptidase with thrombospondin type 1 motif, 4 (ADAMTS4) Bt.21021.1.S1_at TBC1 domain family, member 7 (TBC1D7) Bt.2933.1.S1_at Hypothetical protein LOC788205 Bt.9767.1. Squalene epoxidase (SQLE) S1_a_at Bt.621.1.S1_at Cytochrome P450, family 51, subfamily A (CYP51A) Bt.23903.1.A1_at Unknown Bt.22362.1.S1_at SH3-domain kinase binding protein 1 (SH3KBP1) Bt.16752.1.A1_at ATP binding protein (TXNDC9) Bt.1020.1.S1_at CDC-like kinase 1 (CDClk1) Bt.19107.2.A1_at Transcribed locus Bt.28011.1.S1_at Unknown Bt.22718.1.A1_at Proteasome (prosome, macropain) activator subunit 4 (PSME4) Bt.19107.1.S1_at Transcribed locus Bt.25102.1. Hypothetical LOC509649 S1_a_at Bt.22038.1. Arginyl-tRNAsynthetase (RARs) S1_a_at Bt.21268.1.S2_at Ribosomal protein S6 kinase, 70 kDa (TUBD1) Bt.13342.1.S1_at Src-associated protein SAW (UTP15) Bt.344.1.S1_at Major histocompatibility complex, class II (BOLA-DMA) Bt.21827.2.S1_at Thimetoligopeptidase 1 (THOP1) Bt.21794.1.S1_at Hypothetical protein LOC777601 Discussion Microarray analysis A major objective of this study was to identify new biolo- gical indicators for marbling in cattle through global Figure 2 Technical validation for microarray results using realtime PCR: Correlation of fold changes between microarray and realtime PCR. 0.855 0.938 0.614 0.982 0.764 0.603 -0.948 -0.903 -0.805 -0.398 -0.432 -0.781 -0.309 -0.515 -0.431 -0.194 0.263 -0.133 -0.168 -1.071 1.241 0.738 0.863 0.822 1.121 0.543 0.981 0.434 0.591 0.729 1.115 0.503 0.469 -0.343 -0.299 -0.829 -1.152 -0.595 -0.679 -0.376 -0.451 -0.583 -0.631 -1.212 -1.213 -0.312 -0.357 -0.598 -0.813 -0.515 -0.544 0.471 0.643 -0.462 -0.555 -0.537 -1.081 -0.531 -0.856 0.863 1.272 0.818 0.0006 0.953 0.0037 0.712 0.0084 0.668 0.0013 0.867 0.0048 0.525 0.0080 -0.532 0.0087 -0.960 0.0089 -0.693 0.0123 -0.408 0.0231 -0.548 0.0321 -1.066 0.0376 -0.326 0.0395 -0.642 0.0729 -0.496 0.0824 0.0002 0.0005 0.0003 0.0005 0.0028 0.0017 0.0015 0.0047 0.0001 0.00002 0.0081 0.0178 0.0062 0.0232 0.0090 0.0231 0.0051 0.0006 0.0018 0.00005 0.0024 0.0012 0.0022 0.0051 0.0087 0.0048 0.0012 0.0045 0.0033 0.0046 0.459 0.1632 -0.383 0.2981 -0.595 0.3762 -0.818 0.0045 1.124 0.0046 0.0045 0.0012 0.0011 0.0004 0.0069 0.0035 0.0087 0.0162 0.0050 0.0149 -0.238 -0.213 -0.215 0.1321 0.0055 0.0045 transcription profiling (24K Affymetrix chip). Identifica- tion of novel differentially expressed genes might allow a better understanding of the complex biochemical mechanisms of marbling in cattle. To date, microarray based gene expression analyses for beef meat quality (marbling) have focused on detecting differentially expressed genes in different breeds of cattle such as Japa- nese Black (Wagyu) and Holstein Friesian cattle for a wide range of marbling phenotypes [12,15]. As expected, many lipid metabolism related genes (for example, FABP4 and SCD) were highly expressed in the Japanese Black. As Pethick [2] commented, visible intramuscular fat content is a late maturing trait in cattle. Therefore, this study attempted to investigate genes that are differ- entially expressed in divergent marbling phenotypes at late stages of cattle growth. So far, a well-known biochemical finding in relation to marbling expression in muscle was presented by Jurie et al. [16], who repored that fatty acid binding protein 4 activity was strongly correlated with intramuscular fat content. In their study they compared the different genetic performance of intramuscular fat deposition