Clustering of protein expression data: a benchmark of statistical and neural approaches

Clustering issues are fundamental to exploratory analysis of bioinformatics data. This process may follow algorithms that are reproducible but make assumptions about, for instance, the ability to estimate the global structure by successful local agglomeration or alternatively, they use pattern recognition methods that are sensitive to the initial conditions. This paper reviews two clustering methodologies and highlights the differences that result from the changes in data representation, applied to a protein expression data set for breast cancer (n = 1,076). The two clustering methodologies are a reproducible approach to model-free clustering and a probabilistic competitive neural network. The results from the two methods are compared with existing studies of the same data set, and the preferred clustering solutions are profiled for clinical interpretation.