X2K

X2K is a software tool that provides a novel approach to identifying upstream regulators responsible for observed patterns in genome-wide gene expression. The motivation behind X2K is to understand better the complex regulatory mechanisms that govern gene expression, as mRNA levels alone do not provide a direct understanding of upstream regulatory mechanisms.

X2K integrates various data types, such as chromatin immuno-precipitation (ChIP)-seq/chip and position weight matrices (PWMs) data, protein-protein interactions, and kinase-substrate phosphorylation reactions. By doing so, it can more accurately identify regulatory mechanisms upstream of genome-wide differences in gene expression.

The software has been validated and tested in a variety of applications, such as recovering drug targets of FDA-approved drugs from drug perturbations followed by mRNA expression profiling, mapping the regulatory landscape of stem cells and their differentiating progeny, profiling upstream regulatory mechanisms of breast cancer tumors, and detecting pathways in hepatic stellate cells and hippocampal neurons.