Fig. 1. Experiments that establish relationships between genes, proteins, cells and functions. Most genome-wide data sets describe biological entities or draw connections between entities. For example, DNA sequence is linked to genes by gene prediction and experimental annotation (e.g. cDNA sequencing). Genes are associated with other genes by genetic interactions. Proteins are related by physical binding, e.g. as detected in yeast two-hybrid assays. Proteins are shown to interact with DNA through chromatin-immunoprecipitation (ChIP) and yeast one-hybrid assays (e.g. Deplancke et al., 2006). Genes and protein are assigned functions based on perturbations (mutations, overexpression, RNAi). Cells are associated with genes and proteins by gene expression. Cells (or tissues) are associated with functions by mechanical (e.g. laser ablation) or genetic (e.g. mutation) lesion experiments or by generating genetic mosaics.