Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach

TL;DR

This paper introduces a Bayesian hierarchical model to identify perturbed biological pathways from gene expression data, effectively capturing complex network interactions and outperforming traditional methods in detecting causative pathways.

Contribution

The authors develop a novel three-level hierarchical Bayesian model that integrates gene expression, pathway networks, and perturbation detection, advancing pathway analysis methods.

Findings

Successfully identified causative regulatory pathways.

Outperformed gene set enrichment analysis in accuracy.

Demonstrated robustness to database inaccuracies.

Abstract

Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell's fate. Here our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge data set. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases.