Pineda, AL, Gopalakrishnan, V. Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. Proceedings of the AMIA Translational Bioinformatics Summit. March 21-23, 2015. PMID: 26306226 Winner of the Marco Ramoni Distinguished Paper Award.
In this era of precision medicine, understanding the epigenetic differences in lung cancer subtypes could lead to personalized therapies by possibly reversing these alterations. Traditional methods for analyzing microarray data rely on the use of known pathways. We propose a novel workflow, called Junction trees to Knowledge (J2K) framework, for creating interpretable graphical representations that can be derived directly from in silico analysis of microarray data. Our workflow has three steps, preprocessing (discretization and feature selection), construction of a Bayesian network and, its subsequent transformation into a Junction tree. We used data from the Cancer Genome Atlas to perform preliminary analyses of this J2K framework. We found relevant cliques of methylated sites that are junctions of the network along with potential methylation biomarkers in the lung cancer