The connection is represented as an arc and is defined as a relationship between two biological variables (phenotypes, pathways, diseases etc.), to suit the particular question that the user has in mind. For instance, a connection between two phenotypes can mean that these phenotypes share some genes involved in a particular pathway or process or it can mean that there is a transition between these two phenotypes for at least one gene event. In general, the arc will indicate how many genes/proteins with values above a certain threshold are shared between the two phenotypes/pathways.
The color of the arcs gives the directionality of the connection where needed (i.e. in the case when it represents a transition from one time point to the other). It indicates the end phenotype.
The height of the arc is proportional to the number of genes/proteins or other genetic events for which that connection appears at a particular time point.