RNA-Seq analysis of C. parapsilosis cells.

Lists of genes differentially expressed in C. parapsilosis CLIB214 cells grown in synthetic media containing 3-hydroxybenzoate, 4-hydroxybenzoate or hydroquinone compared to the cells assimilating galactose (i.e. S3OH vs. SGal, S4OH vs. SGal, SHyd vs. SGal) or 4-hydroxybenzoate (S3OH vs. S4OH, SHyd vs. S4OH). The estimate of fold expression change was computed by DESeq2 [77] based on three replicates of each growth condition. DESeq2 uses a generalized linear model and empirical Bayes shrinking to estimate log2 fold expression change and the standard error of this estimate; the p-value of a gene being differentially expressed is then obtained using a Wald test based on the z-score of the log2 fold change as the test statistics (multiple testing correction by false discovery rate method). The base mean is the average of count values over all experiments, normalized by library size factors. (XLSX)