Johns Hopkins School of Medicine
To whom correspondence should be addressed. E-mail : deepsilence(at).jhmi.edu
Various approaches and technologies have emerged to understand the functional regulatory elements in the genome. They provide rich resources to biomedical researchers in better understanding the systems aspect of biology. However, the underlying approaches, assumptions and strengths and weaknesses are often less appreciated. Here we overview two general approaches that tackle the problem of identifying functional regulatory elements. The first approach is to infer regulatory elements de novo from similarity of expression or homology within phylogeny. The other approach is to focus on a particular mode of regulatory mechanism and construct a biophysical model based on high-throughput genome-wide data to predict interaction. A notable example is the prediction of transcription factor binding sites (TFBS). Practical resources, such as major databases and prediction algorithms are briefly evaluated as guides for general researchers.
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