A Primer on Regression Methods for Decoding cis-Regulatory Logic: e1000269

Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4]-[6]--in particular, by integrating sequence data with mRNA expression profiles. [...]the combinatorial nature of gene regulation is difficult to explicitly model in this framework. [...]in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. [...]although most regression methods are used to model the observed changes in gene expression between a pair of conditions, recently this methodology has been extended to include information from multiple conditions as well [29].