Differential expression analysis of the in vitro and rabbit samples.

Average normalized RNA-seq counts, log2-fold difference values (combined rabbit/in vitro), and adjusted p-values (combined rabbit vs. in vitro) obtained for T. pallidum subsp. pallidum Nichols during in vitro culture and rabbit infection. T. pallidum ORF numbers, gene IDs, and coordinates are from NCBI RefSeq entry NC_021490. ORF numbers in blue indicate genes with significantly higher transcript levels in infected rabbits, while ORF numbers in orange indicate genes with significantly higher transcript levels in vitro. * Functional roles based on Gene Ontology (GO) terms (QuickGO). Unless otherwise indicated, functional categories based on [26]. (XLSX)