Neighborhood-based clustering of gene-gene interactions

Abstract

In this work, we propose a new greedy clustering algorithm to identify groups of related genes. Clustering algorithms analyze genes in order to group those with similar behavior. Instead, our approach groups pairs of genes that present similar positive and/or negative interactions. Our approach presents some interesting properties. For instance, the user can specify how the range of each gene is going to be segmented (labels). Some of these will mean expressed or inhibited (depending on the gradation). From all the label combinations a function transforms each pair of labels into another one, that identifies the type of interaction. From these pairs of genes and their interactions we build clusters in a greedy, iterative fashion, as two pairs of genes will be similar if they have the same amount of relevant interactions. Initial two-genes clusters grow iteratively based on their neighborhood until the set of clusters does not change. The algorithm allows the researcher to modify all the criteria: discretization mapping function, gene-gene mapping function and filtering function, and provides much flexibility to obtain clusters based on the level of precision needed. The performance of our approach is experimentally tested on the yeast dataset. The final number of clusters is low and genes within show a significant level of cohesion, as it is shown graphically in the experiments. © Springer-Verlag Berlin Heidelberg 2006.