Factor analysis for gene regulatory networks and transcription factor activity profiles

Background: Most existing algorithms for the inference of the structure of gene regulatory networks from gene expression data assume that the activity levels of transcription factors (TFs) are proportional to their mRNA levels. This assumption is invalid for most biological systems. However, one might be able to reconstruct unobserved activity profiles of TFs from the expression profiles of target genes. A simple model is a two-layer network with unobserved TF variables in the first layer and observed gene expression variables in the second layer. TFs are connected to regulated genes by weighted edges. The weights, known as factor loadings, indicate the strength and direction of regulation. Of particular interest are methods that produce sparse networks, networks with few edges, since it is known that most genes are regulated by only a small number of TFs, and most TFs regulate only a small number of genes. Results: In this paper, we explore the performance of five factor analysis alg...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Iosifina Pournara, Lorenz Wernisch
• Keywords: BMCBI 2007, Gene Regulatory Network, Matrix Rotation Methods, Most Existing Algorithms