Nayfach Stephen, Fischbach Michael A, Pollard Katherine S
Integrative Program in Quantitative Biology, Gladstone Institutes, and Division of Biostatistics, University of California San Francisco and.
Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA, USA.
Bioinformatics. 2015 Oct 15;31(20):3368-70. doi: 10.1093/bioinformatics/btv382. Epub 2015 Jun 22.
Microbiome researchers frequently want to know how abundant a particular microbial gene or pathway is across different human hosts, including its association with disease and its co-occurrence with other genes or microbial taxa. With thousands of publicly available metagenomes, these questions should be easy to answer. However, computational barriers prevent most researchers from conducting such analyses. We address this problem with MetaQuery, a web application for rapid and quantitative analysis of specific genes in the human gut microbiome. The user inputs one or more query genes, and our software returns the estimated abundance of these genes across 1267 publicly available fecal metagenomes from American, European and Chinese individuals. In addition, our application performs downstream statistical analyses to identify features that are associated with gene variation, including other query genes (i.e. gene co-variation), taxa, clinical variables (e.g. inflammatory bowel disease and diabetes) and average genome size. The speed and accessibility of MetaQuery are a step toward democratizing metagenomics research, which should allow many researchers to query the abundance and variation of specific genes in the human gut microbiome.
http://metaquery.docpollard.org.
snayfach@gmail.comS UPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
微生物组研究人员常常想了解特定微生物基因或途径在不同人类宿主中的丰度，包括其与疾病的关联以及与其他基因或微生物分类群的共现情况。有了数千个公开可用的宏基因组，这些问题应该很容易回答。然而，计算障碍使得大多数研究人员无法进行此类分析。我们通过MetaQuery解决了这个问题，MetaQuery是一个用于快速定量分析人类肠道微生物组中特定基因的网络应用程序。用户输入一个或多个查询基因，我们的软件会返回这些基因在来自美国、欧洲和中国个体的1267个公开可用粪便宏基因组中的估计丰度。此外，我们的应用程序会进行下游统计分析，以识别与基因变异相关的特征，包括其他查询基因（即基因共变异）、分类群、临床变量（如炎症性肠病和糖尿病）以及平均基因组大小。MetaQuery的速度和可访问性朝着使宏基因组学研究民主化迈出了一步，这应该能让许多研究人员查询人类肠道微生物组中特定基因的丰度和变异情况。
http://metaquery.docpollard.org。
补充数据可在《生物信息学》在线获取。
