Supplemental material for Hogle et al. 2015 mBio
收藏资源简介：
<strong>Publication reference:</strong> "Trace metal acquisition by heterotrophic bacterioplankton with contrasting trophic strategies" <strong>Available at mBio website, Figshare.com, and slhogle.github.io :</strong><br>Dataset1.xlsx - Genome features, Genome completion, environmental characteristics, transporter abundance<br>Dataset2.xlsx - CDD/PFAM/COGs used to identify metal transporters<br>Dataset3.xlsx - Predicted FUR boxes<br>Dataset4.xlsx - COGs for Tree Construction TableS1.pdf - Metal transporter families and descriptions TableS2.pdf - TBDT Clusters and enrichment FigureS1.pdf - TRAP transporters in siderophore uptake genome neighborhoods<br>FigureS2.pdf - Network visualization of pairwise Spearman's rank correlation coefficients supplemental_text.pdf - Supplementary results and methods <strong>Available only at Figshare.com and slhogle.github.io</strong><br>DatasetS5.xlsx - TBDT neighborhoods, and Markov Clustering parameters<br>DatasetS6.xlsx - SAR11 IMG genome cart export<br>DatasetS7.xlsx - Roseobacter IMG genome cart export<br>DatasetS8.xlsx - Particle associated versus free-living lifestyle assignments and references used to make assignments<br>DatasetS9.xlsx - Pairwise false discovery rate corrected Spearman's rank correlation coefficients scripts - folder with scripts and markdown used to do analysis
参考文献：《具有差异化营养策略的异养浮游细菌微量金属获取机制》<br>可从mBio官网、Figshare平台及slhogle.github.io获取：<br>数据集1.xlsx：基因组特征、基因组完整性、环境特征、转运蛋白丰度<br>数据集2.xlsx：用于鉴定金属转运蛋白的CDD（保守结构域数据库，Conserved Domain Database）、PFAM（蛋白质家族数据库，Protein Family Database）及COGs（直系同源簇，Clusters of Orthologous Groups）注释集<br>数据集3.xlsx：预测的FUR结合基序（铁摄取调节因子结合基序，Ferric uptake regulator, FUR）<br>数据集4.xlsx：用于构建系统发育树的COGs注释集<br>表S1.pdf：金属转运蛋白家族及功能说明<br>表S2.pdf：TBDT簇（TonB依赖性转运蛋白簇，TonB-dependent transporter, TBDT）与富集分析结果<br>图S1.pdf：铁载体摄取基因组邻域中的TRAP转运蛋白（三组分ATP非依赖性周质转运蛋白，Tripartite ATP-independent periplasmic transporter, TRAP）<br>图S2.pdf：两两斯皮尔曼等级相关系数的网络可视化<br>补充文本.pdf：补充结果与方法<br>仅可从Figshare平台及slhogle.github.io获取：<br>数据集S5.xlsx：TBDT基因组邻域及马尔可夫聚类（Markov Clustering）参数<br>数据集S6.xlsx：SAR11类群IMG基因组工作台（整合微生物基因组数据库工作台，Integrated Microbial Genomes, IMG）导出文件<br>数据集S7.xlsx：玫瑰杆菌（Roseobacter）类群IMG基因组工作台导出文件<br>数据集S8.xlsx：颗粒附着型与自由生活型生活方式归类及归类依据的参考文献<br>数据集S9.xlsx：经过错误发现率（False Discovery Rate, FDR）校正的两两斯皮尔曼等级相关系数<br>脚本文件夹：包含本分析所用的脚本与Markdown文档
