期刊
BRIEFINGS IN FUNCTIONAL GENOMICS
卷 12, 期 4, 页码 366-380出版社
OXFORD UNIV PRESS
DOI: 10.1093/bfgp/elt008
关键词
genotype-phenotype association; genome-wide association studies; functional genomics; microbial genomics; random forest
资金
- Netherlands Organisation for Scientific Research (NWO) [016.111.075]
- NSF from Division of Biological Infrastructure [DBI: 0850356]
- NSF from Division of Environmental Biology [DEB: 1046413]
- Dutch e-Science Grid (BiG Grid)
- NWO
- Direct For Biological Sciences [1046413, 0850356] Funding Source: National Science Foundation
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.
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