1. A computer-implemented method for visualizing flows through at least a first application, the method comprising: accessing a data store to access data regarding the first application, the data is obtained from an agent associated with the first application using instrumentation which is installed in the first application, the data represents multiple instances of the first application; displaying a dependency graph on a user interface, the dependency graph graphically depicts: (a) a first node which represents the multiple instances of the first application, (b) a second node which represents one subsystem on which the first application depends when a first preselected component of the first application is invoked, the first application is invoked in a first business transaction by virtue of the first preselected component being invoked, (c) at least one edge which represents a dependency of the first application on the one subsystem, (d) a node which represents another subsystem on which the first application depends when a second preselected component of the first application is invoked, the first application is invoked in a second business transaction by virtue of the second preselected component being invoked, and (e) another edge which represents a dependency of the first application on the another subsystem; and responsive to a user selection of the first business transaction: visually distinguishing the node which represents the one subsystem from the node which represents the another subsystem, and visually distinguishing the one edge from the another edge.