Inferring Gene Dependency Networks from Genomic Longitudinal Data: a Functional Data Approach

Abstract

A key aim of systems biology is to unravel the regulatory interactions among genes and gene products in a cell. Here we investigate a graphical model that treats the observed gene expression over time as realizations of random curves. This approach is centered around an estimator of dynamical pairwise correlation that takes account of the functional nature of the observed data. This allows to extend the graphical Gaussian modeling framework from i.i.d. data to analyze longitudinal genomic data. The new method is illustrated by analyzing highly replicated data from a genome experiment concerning the expression response of human T-cells to PMA and ionomicin treatment.

Keywords

• graphical model
• longitudinal data
• dynamical correlation
• gene dependency networks