MOESM5 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

Additional file 5. Sorted gene expression tables of top 100 genes by relative expression. Average gene length-normalized expression values (FPKM, calculated by SeqMonk) for the short-term and long-term coincidence cloning samples, generated as described in Additional file 4, were sorted by expression level for the short-term (left-hand columns) or the long-term (right-hand columns) samples. COG (Cluster of Orthologous Group) designations, as determined via the PHIDIAS Brucella Bioinformatics Portal ( www.phidias.us/bbp/ ), are annotated. The top 100 genes from each group in expression levels are provided. We note that there are challenges with the use of read data in FPKM/RPKM averaged across multiple samples, as discussed by Wagner et al. [67]. However, as depicted in Additional file 4, average FPKM values for each sample were very similar between biological replicates. We also completed an analysis in which the rank orders of gene expression were determined for each individual sample, and then genes were sorted by the lowest average rank order of expression. 96% of the long-term top 100 genes and 90% of the short-term top 100 genes were identical between the two methods. COG category single letter associations: amino acid transport and metabolism (E), carbohydrate transport and metabolism (G), cell cycle control and cell division, chromosome partitioning (D), cell motility (N), cell wall/membrane/envelope biogenesis (M), chromatin structure and dynamics (B), coenzyme transport and metabolism (H), cytoskeleton (Z), defense mechanisms (V), energy production and conversion (C), extracellular structures (W), function unknown (S), general function and prediction only (R), inorganic ion transport and metabolism (P), intracellular trafficking, secretion and vesicular transport (U), lipid transport and metabolism (I), nucleotide transport and metabolism (F), post-translational modification, protein turnover, chaperones (O), RNA processing and modification (A), replication, recombination and repair (L), secondary metabolites biosynthesis, transport and catabolism (Q), signal transduction mechanisms (T), transcription (K), translation, ribosomal structure and biogenesis (J)