Interspecies Differential Gene Expression Analysis with Regularized Phylogenetic Linear Models

phyloDE, an inter-species RNA-Seq differential expression method, correctly controls the False Discovery Rate in simulations based on a four-species rodent dataset while maintaining reasonable power.

• Why it matters: Random evolutionary drift and phylogenetic correlations can inflate FDR, and standard RNA-Seq DE tools and classical phylogenetic models each address only one of these problems.
• What they did: The R tool phyloDE uses regularized phylogenetic linear models for inter-species DE, and it was benchmarked on simulations derived from a recently published four-species rodent dataset.
• The result: In reanalysis of the empirical four-species rodent dataset, phyloDE identifies more differentially expressed genes with consistent cis-regulatory changes than EVE across experimental settings.

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