Empirically determining the sample size for large-scale gene network inference algorithms

The performance of genome-wide gene regulatory network inference algorithms depends on the sample size. It is generally considered that the larger the sample size, the better the gene network inference performance. Nevertheless, there is not adequate information on determining the sample size for optimal performance. In this study, the author systematically demonstrates the effect of sample size on information-theory-based gene network inference algorithms with an ensemble approach. The empirical results showed that the inference performances of the considered algorithms tend to converge after a particular sample size region. As a specific example, the sample size region around ≃64 is sufficient to obtain the most of the inference performance with respect to precision using the representative algorithm C3NET on the synthetic steady-state data sets of Escherichia coli and also time-series data set of a homo sapiens subnetworks. The author verified the convergence result on a large, real data set of E. coli as well. The results give evidence to biologists to better design experiments to infer gene networks. Further, the effect of cutoff on inference performances over various sample sizes is considered. [Includes supplementary material].