Using graphs to relate expression data and protein-protein interaction data

In Ge et al. (2001) the authors consider an interesting question. They assemble gene expression data from a yeast cell-cycle experiment (Cho et al., 1998), literature proteinprotein interaction (PPI) data and yeast two-hybrid data. We have curated the data slightly to make it simpler to carry out the analyses reported in Ge et al. (2001). In particular we reduced the data to the 2885 genes that were common to all experiments. We have also represented most of the data in terms of graphs (nodes and edges) since that is the form we will use for most of our analyses. The results reported in this document are based on version 0.9.23 of the yeastExpData data package.