ABSTRACT
Combining information from multiple domains can provide meaningful answers to important biological questions. The domains (or “experiments,” a term which we use interchangeably with “domains” throughout this chapter) involved might address the same scientific hypothesis, or a range of different but related hypotheses. We restrict attention to situations in which the multiple experiments aim to determine common genetic variants across multiple stimuli, such as cross-stimulus and cross-species studies. For example, one might wish to find:
1. genes that are differentially expressed in response to a particular stimulus across several experimental crosses or different tissue types within the same cross,
2. genes that are differentially expressed in a similar pattern in response to multiple stimuli, or
3. genes that independently influence two or more phenotypic traits (i.e., pleiotropy).
