For example, to study stress response an experimenter may measure mRNA levels for all transcripts, key protein levels before and after the stress event. They could then compare these data across individuals with genetic differences. By noticing associations between certain genotypes and subsequent mRNA and protein response the experimenter can draw conclusions about which genes have a role in regulating stress response and how they work through transcription and translation.
Many things to many people. Broadly speaking, the subject is a combination of multiple fields to solve a global question. Rather than reducing problems to small, solvable components the field seeks to take a 'big picture' approach and understand the various interacting roles involved.