Title: Confounding effects in gene expression and their impact on downstream analysis
Description: The reconstruction of gene regulatory networks is one of the milestones of computational system biology. We introduce a new implementation of ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) to reverse engineer transcriptional regulatory networks with improved mutual information estimators and significant improvement in performance. In the context of data driven network inference we identify two major confounding biases and introduce solutions to remove some of the discussed biases. First we identify prevalent spatial biases in gene expression studies derived from plate based designs. We investigate the gene expression profiles of a million samples from the LINCS dataset and find that the vast majority (96%) of the tested plates is affected by significant spatial bias. We can show that our proposed method to correct these biases results in a significant improvement of similarity between biological replicates assayed in different plates. Lastly we discuss the effect of CNV on gene expression and its confounding effect on the correlation landscape of genes in the context of cancer samples.

We propose a method that removes the variance in gene expression explained by CNV and show that TF target predictions can be significantly improved.