Mathematical Programming for Modeling Expression of a Gene Using Gurobi Optimizer to Identify Its Transcriptional...

The cell expresses various genes in specific contexts with respect to internal and external perturbations to invoke appropriate responses. Transcription factors (TFs) orchestrate and define the expression level of genes by binding to their regulatory regions. Dysregulated expression of TFs often leads to aberrant expression changes of their target genes and is responsible for several diseases including cancers. In the last two decades, several studies experimentally identified target genes of several TFs. However, these studies are limited to a small fraction of the total TFs encoded by an organism, and only for those amenable to experimental settings. Experimental limitations lead to many computational techniques having been proposed to predict target genes of TFs. Linear modeling of gene expression is one of the most promising computational approaches, readily applicable to the thousands of expression datasets available in the public domain across diverse phenotypes. Linear models assume that the expression of a gene is the sum of expression of TFs regulating it. In this chapter, I introduce mathematical programming for the linear modeling of gene expression, which has certain advantages over the conventional statistical modeling approaches. It is fast, scalable to genome level and most importantly, allows mixed integer programming to tune the model outcome with prior knowledge on gene regulation.