Graph-centric approaches to metatranscriptomic and metaproteomic data analysis

描述（由申请人提供）：虽然元基因组学可以揭示微生物群落的遗传组成（从而揭示遗传潜力），但其他元基因组学（例如，元转录组学和元蛋白质组学）技术可以提供关于群落功能特征的额外见解，例如基因活性及其调控机制。分析这些功能性微生物组数据集提出了新的计算挑战。在本应用中，我们提出了一种新的方法来进行元基因组和元蛋白质组数据分析，使用元基因组组装的de Bruijn图表示作为参考，从而实现对元基因组数据集的集成分析。使用de Bruijn图的优点包括：1)它们提供了宏基因组（可能是冗余的）的紧凑表示，并允许在图上直接计算；2)它们自然地捕获基因组变异；3)它们捕获了contigs/scaffold之间的“模糊”连接，这可以在后续步骤中使用额外的信息来解决，或者利用元转录组学和元蛋白质组学数据分别实现更好的基因和蛋白质鉴定和定量。我们将应用我们的新工具来分析功能性人类微生物组数据集，包括那些将从HMP二期项目中产生的数据集。

DESCRIPTION (provided by applicant): While metagenomics can reveal genetic composition (and therefore the genetic potential) of microbial communities, other meta-omic (e.g., metatranscriptomic and metaproteomic) techniques can provide additional insights on functional characteristics of the communities, such as gene activities and their regulation mechanisms. Analyzing these functional microbiome data sets raises new computational challenges. In this application, we propose novel approaches to metatranscriptomic and metaproteomic data analyses, using de Bruijn graph representations of metagenome assemblies as the reference, enabling an integrated analysis of meta-omic data sets. The advantages of using de Bruijn graphs include: 1) they provide a compact representation of metagenomes (which are likely to be redundant) and allow direct computation on the graph, 2) they naturally capture genomic variations; and 3) they capture the "ambiguous" connectivity between contigs/scaffolds, which can be resolved in subsequent steps using additional information, or utilized to achieve better identification and quantification of genes and proteins using metatranscriptomic and metaproteomic data, respectively. We will apply our new tools to analyzing functional human microbiome data sets, including those to be generated from HMP phase II projects.