What does expand/collapse mean in the Onto-Express output?
The terms “expand” and “collapse” refer to the state of a GO term in the tree-view of Onto-Express. They are related to the DAG nature of GO. In the “expand” mode, OE only considers the genes specifically annotated with the given term, and ignores the genes annotated with the children terms. In the “collapse” mode, for a given term, OE considers the genes annotated with its children terms as also being annotated with the given term. For instance, let us assume that the term “apoptosis” is a parent of the term “induction of apoptosis”. Further, let us assume that a gene A is annotated with the term apoptosis and a gene B is annotated with the term induction of apoptosis. In the expand mode the total number of genes for both terms is 1. However, if a term is collapsed, all genes annotated with the children term are now considered to be annotated with the collapsed term (i.e., the parent term). Hence, if the term apoptosis is collapsed, the gene B, which is annotated with induction of apo
