Core C. Bioinformatics and data sharing.

核心C，摘要 尽管结核分枝杆菌（Mtb）的基因组首次被发现已经有20多年了， 尽管基因组测序的结果表明，基因组中超过一半的基因的功能仍然未知（或不清楚）。额外来源 为了更好地理解特定的生物学作用， 结核基因在基本的细胞过程和感染中起作用。在这个项目中，四种疾病相关的途径 将研究：对酸性胁迫的代谢反应，生物素生物合成，RNA加工和细胞分裂。的 该项目将严重依赖的四种实验方法是转座子测序（TnSeq; essentiality）， RNAseq（转录组学）、基于活性的代谢组学分析（ABMP）和CRISPR干扰（CRISPRi）。 TnSeq和RNAseq将应用于靶基因的敲除或敲低菌株，以评估细胞内的 这些扰动的反应，并推断新的基因功能和途径协会。测序 转座子插入库（TnSeq）提供了一种强大的方法来探测功能和关系 通过条件必要性和遗传相互作用。CRISPRi将用于生成 敲低菌株以验证TnSeq预测的表型。转录组学数据产生关于共- 表达，其可用于推断功能关系，例如通过调节网络。ABMP提供 通过代谢物浓度的变化（例如，可能的底物或 产品）。 生物信息学和数据共享核心的作用是协助项目进行严格的统计， 分析这些数据。具体而言，在活动1中，核心将对各种组学进行生物信息学分析， 数据库，以确定新的基因在目标途径，并确定其功能作用。活动2核心 我将应用机器学习算法来整合这些不同的组学数据库并建立预测模型 可以用来识别这些途径中的新基因并预测它们的功能。最后，在活动3下， 生物信息学和数据共享核心将作为数据共享的集中渠道;包括存放 在适当的公共储存库中收集数据，并在它们开发的一个专门用于结核病的网站上公布数据。

Core C, Abstract Even though it has been over 20 years since the genome of Mycobacterium tuberculosis (Mtb) was first sequenced, the functions of over half the genes in the genome remain unknown (or unclear). Additional sources of information (beyond homology) are needed to generate a better understanding of the specific biological roles Mtb genes play in basic cellular processes and infection. In this program project, four disease-relevant pathways will be studied: metabolic response to acidic stress, biotin biosynthesis, RNA processing, and cell division. The four experimental methods that the Projects will rely heavily on are transposon sequencing (TnSeq; essentiality), RNAseq (transcriptomics), Activity-Based Metabolomic Profiling (ABMP), and CRISPR interference (CRISPRi). TnSeq and RNAseq will be applied to knockout or knockdown strains of target genes to assess the intracellular responses to these perturbations and infer novel gene functions and pathway associations. Sequencing of transposon insertion libraries (TnSeq) provides a powerful method for probing the functions and relationships among genes through conditional essentiality and genetic interactions. CRISPRi will be used to generate knockdown strains to validate phenotypes predicted by TnSeq. Transcriptomic data yields information on co- expression, which can be used to infer functional relationships, e.g. through regulatory networks. ABMP provides direct information on gene functions through changes in metabolite concentrations (e.g. possible substrates or products) when purified protein is incubated in lysate. The role of the Bioinformatics and Data Sharing Core is to assist the Projects with rigorous statistical analyses of these data. Specifically, in Activity 1 the Core will conduct bioinformatic analysis of various 'omics datatypes to identify novel genes in the target pathways and define their functional roles. In Activity 2 the Core will apply Machine Learning algorithms to integrate these diverse 'omics datatypes and build predictive models that can be used to identify new genes in these pathways and predict their functions. Finally, under Activity 3 the Bioinformatics and Data Sharing Core will serve as a centralized conduit for data sharing; including depositing datasets in appropriate public repositories, and posting data on an Mtb-dedicated website they have developed.