Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data

Miguel Lopes, Gianluca Bontempi

Accurate inference of causal gene regulatory networks from gene expression data is an open bioinformatics challenge. Gene interactions are dynamical processes and consequently we can expect that the effect of any regulation action occurs after a certain temporal lag. However such lag is unknown a priori and temporal aspects require specific inference algorithms. In this paper we aim to assess the impact of taking into consideration temporal aspects on the final accuracy of the inference procedure. In particular we will compare the accuracy of static algorithms, where no dynamic aspect is considered, to that of fixed lag and adaptive lag algorithms in three inference tasks from microarray expression data. Experimental results show that network inference algorithms that take dynamics into account perform consistently better than static ones, once the considered lags are properly chosen. However, no individual algorithm stands out in all three inference tasks, and the challenging nature of network inference tasks is evidenced, as a large number of the assessed algorithms does not perform better than random.