Extended Data Fig. 2: Number of genes that showed significant DE in Cog functional categories.
The number of significant DE genes, using a p-adjusted \(\le\) 0.05, and a log2 fold change ≥ |−1|, grouped according to Cog functional categories. Red bars indicate the number of genes that showed a relative increase in expression, blue bars indicate the number of genes that showed a relative decrease in expression. Log2 fold change calculated using limma package in R with a two-sided linear model fit followed by empirical Bayes moderation of the standard errors (using the eBayes function with robust = TRUE parameter) using the Benjamini-Hochberg method for false discovery rate, controlling for multiple comparisons. Comparison of aquaria conditions represented by letters on top row (for abbreviation key see Fig. 1 and Supplementary Table 1). For details on aquaria conditions see Supplementary Table 1. Cog functional category abbreviations listed below: T-Signal transduction L-Replication and repair E-Amino acid metabolism/transport. P-Inorganic ion transport/metabolism K-Transcription D-Cell cycle control and mitosis. O-Post-translational modification/protein turnover J-Translation C-Energy production/conversion. N-Cell motility G-Carbohydrate metabolism/ transport. M-Cell membrane biogenesis.
