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).

附加文件5：按相对表达量排序的前100个基因的基因表达表。
按照附加文件4所述方法生成的短期与长期共克隆样本的经基因长度归一化平均表达值（FPKM，由SeqMonk软件计算），分别按短期样本（左侧列）与长期样本（右侧列）的表达水平进行排序。通过PHIDIAS布鲁氏菌生物信息学门户（www.phidias.us/bbp/）确定的直系同源簇（Cluster of Orthologous Group, COG）注释信息也一并标注。本文件提供了两组中各前100个高表达基因。
我们注意到，正如Wagner等人[67]所述，对多个样本的FPKM/RPKM读取数据进行平均处理存在一定局限性。但如附加文件4所示，生物学重复样本的平均FPKM值高度相似。我们还开展了一项分析：先对每个独立样本的基因表达秩次进行判定，再以平均秩次最低的标准对基因进行排序。结果显示，两种方法得到的长期前100个基因重合率达96%，短期前100个基因重合率达90%。
COG类别的单字母对应关系如下：氨基酸转运与代谢（E）、碳水化合物转运与代谢（G）、细胞周期调控、细胞分裂及染色体分离（D）、细胞运动性（N）、细胞壁/细胞膜/被膜生物发生（M）、染色质结构与动态（B）、辅酶转运与代谢（H）、细胞骨架（Z）、防御机制（V）、能量产生与转化（C）、细胞外结构（W）、功能未知（S）、一般功能预测（R）、无机离子转运与代谢（P）、细胞内运输、分泌与囊泡运输（U）、脂质转运与代谢（I）、核苷酸转运与代谢（F）、翻译后修饰、蛋白质周转与分子伴侣（O）、RNA加工与修饰（A）、复制、重组与修复（L）、次级代谢产物生物合成、转运与分解代谢（Q）、信号转导机制（T）、转录（K）、翻译、核糖体结构与生物发生（J）。