Bioinformatics and Biomarker Discovery: "Omic" Data Analysis for Personalized Medicine

Guest commentary on chapter 6: Data integration in proteomics and metabolomics for biomarker discovery

Kenneth Bryan

Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland

Advances in both proteomics and metabolomics analyses over recent years have added greatly to our genome-wide view of transcription provided by the advent of microarray gene expression analysis. With proteomics, the first step in the expression of the phenotype, the transcriptome, can now be augmented with information on post-transcriptional regulation. Indeed recent advances in our understanding of post-transcriptional regulation have made measurement of this stage of expression more relevant than ever. Small, regulating RNAs known as microRNAs (miRNA), have now been shown to be critical regulators of translation for many proteins and to be involved in the progression of many diseases, including multiple forms of cancer (He and Hannon, 2004). These advances further enforce the assertion that transcription alone does not determine phenotype and that further information on downstream processes are needed to complete the picture. Even after translation a protein may require additional post-translational modification, activation or co-factors before it can perform its designated function. Metabolomics, the global measurement of metabolites and small molecules within a cell or bio-fluid, has recently come of age thanks to advances in experimental platforms (Goodacre et al., 2004). Metabolomics may ...