Protein-Protein Interaction Network Inference (DREAM2, Challenge 2)
For many pairs of bait and prey genes, yeast protein-protein interactions were tested in an unbiased fashion using a high saturation, high-stringency variant of the yeast two-hybrid (Y2H) method. A high confidence subset of gene pairs that were found to interact in at least three repetitions of the experiment but that hadn’t been reported in the literature was extracted. There were 47 yeast genes involved in these pairs. Including self interactions, there are a total of 47*48/2 possible pairs of genes that can be formed with these 47 genes. As mentioned above some of these gene pairs were seen to consistently interact in at least three repetitions of the Y2H experiments: these gene pairs form the "gold standard positive" set. A second set among these gene pairs were seen never to interact in repeated experiments and were not reported as interacting in the literature; we call this the "gold standard negative" set. Finally in a third set of gene pairs, which we shall call the "undecided" set, genes were seen to interact only once or twice in repeated experiments, or were seen never to interact but were reported as interacting in the literature. The challenge consists of predicting which gene pairs belong to the gold standard positive set, and which gene pairs belong to the gold standard negative set.
About the Data
- Data generously provided by Marc Vidal, Dana Farber Cancer Institute
- Reference: Yu H, et. al. High-quality binary protein interaction map of the yeast interactome network. Science. 2008 Oct 3;322(5898):104-10 PubMed
- Yeast Interactome Database
- BioRG_FIU: Hon Nian Chua, Willy Hugo, Guimei Liu, Xiaoli Li, Limsoon Wong, and See-KiongNg, Singapore’s Institute for Infocomm Research and the National University of Singapore.