Additional file 3: of The essential genome of Streptococcus agalactiae

Dataset S2. Detailed Gene Fitness Data. Tab 1 (A909 Final Fitness Assignments) lists A909 genes alongside fitness classification as outlined in the main text. Tabs 2–4 (T0-3 ESSENTIALS Output) show raw data from ESSENTIALS analysis of sequencing data from pooled reads at each of three time points. The columns list (from left to right) gene loci, TA sites per locus, the expected insertion number given the null hypothesis that the gene is nonessential, the log2 FC value for that gene’s experimental vs. expected insertion count, the p value for the FC (generalized linear model likelihood ratio test, corrected for multiple comparisons), start and stop base pair positions for the gene’s ORF, the strand on which the ORF is read, the gene length, its name (if named), and the protein product (if known). Tab 5 (RegPrecise Regulons) lists predicted GBS regulon gene participants. Gene loci are provided for the GBS reference strain 2603 V/R and the A909 homolog. Final fitness category assignments are provided for each gene. Tab 6 (2-Component Systems) shows predicted gene participation in two-component systems identified by P2CS. Columns (from left to right) list GBS gene loci, the original literature description of the gene product function (not necessarily in GBS), the gene’s fitness category assignment, the functional class predicted by domain architecture (either response regulator [RR] or sensor histidine kinase [HK]), and whether the function of the gene or its homolog has been validated experimentally. (XLSX 815 kb)

数据集S2：基因适应度详细数据。表格1（A909最终适应度赋值）列出了A909菌株的全部基因，并附带正文中所述的适应度分类。表格2至4（T0-3 ESSENTIALS输出结果）展示了三个时间点的合并测序读段数据经ESSENTIALS分析得到的原始数据。各列从左至右依次为：基因座位、每个座位的TA位点数量、基于“基因非必需”的零假设所计算的预期插入数、该基因实验插入计数与预期插入计数的log₂FC值、倍变化的p值（经多重比较校正的广义线性模型似然比检验）、该基因开放阅读框（Open Reading Frame, ORF）的起始与终止碱基对位置、开放阅读框的转录链、基因长度、基因名称（若已命名）以及已知的蛋白质产物（若有）。表格5（RegPrecise调控子）列出了预测的B群链球菌（Group B Streptococcus, GBS）调控子参与基因，提供了GBS参考菌株2603 V/R以及A909同源基因的基因座位信息，并为每个基因赋予了最终的适应度分类赋值。表格6（双组分系统（two-component systems））展示了经P2CS鉴定的双组分系统中预测的基因参与情况。各列从左至右依次为：GBS基因座位、基因产物功能的原始文献描述（不一定针对GBS菌株）、该基因的适应度分类赋值、基于结构域架构预测的功能类别（应答调节蛋白（Response Regulator, RR）或组氨酸激酶传感器（Sensor Histidine Kinase, HK）二选一），以及该基因或其同源基因的功能是否经实验验证。（XLSX格式，文件大小815 KB）