Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology

The global behavior of interactions between genes can be investigated by forming the network of functionally-related genes using the annotations based on the Gene Ontology. We define two genes to be connected when the pair of genes is involved in the same biological process. There has been other work on the analysis of different kinds of cellular and metabolic networks, such as gene coexpression network, in which genes are paired when they are found to be coexpressed in the microarray experiments. We observe that our functionally-related gene networks among humans, fruit flies, worms and yeast exhibit the small-world property, but all except the network of worms show the existence of the scale-free property.