Topological analysis of proteomic data

Abstract

Cells become unregulated because topological properties of their interactive behavior make it impossible for them to be regulated. To explore this hypothesis, 2-D PAGE gel electrophoresis protein concentration assay data is embedded and analyzed within a topological computing framework. These 2-D PAGE data are produced using protocols that are standardized, established and widely used. These data are also precise, specific and reliably calibrated alongside an internal reference standard, making the data readily comparable. Importantly, protein concentration data preserve the influence of local interactions, which makes possible a topological analysis. Protein behavior models are developed from longitudinal studies of changes in protein sample concentrations. Continuous variations in protein interactive behavior and their rates of change are shown to produce discontinuous phase shifts in protein concentrations. Preliminary data indicate that a topological analysis of protein data from cancerous cells expose discontinuities in protein behavior space.