Some Notes on Gene Expression and Proteomic Profile Analysis based on Biological Networks

The possibility of using gene expression profiling by microarrays for purposes of diagnostics, prognostics, and understanding the mechanisms of diseases has also generated much excitement in the past decade. Similarly, mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes (Cox and Mann, 2007). It can be applied to better understand cancer pathogenesis and discover indicative biomarkers for early progression. However, a number of issues persist that hamper the effective use of these technologies. In particular, both microarray gene expression profiling and MS-based proteomics have severe consistency issues; and MS-based proteomics additionally have coverage issue. These issues make it difficult to identify genes and proteins that are meaningful in explaining the difference in disease phenotypes (Soh et al., 2007).