Development and Evaluation of Functional Gene Arrays with GeoChip as an Example
Qichao Tu, Ye Deng, Jizhong Zhou and Zhili He
from: Microarrays: Current Technology, Innovations and Applications (Edited by: Zhili He). Caister Academic Press, U.K. (2014)
Functional gene arrays (FGAs) are special microarrays that containing probes targeting functional gene families involved in different microbial functional processes, such as microbially mediated biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorous (P), and metals, biodegradation of organic environmental contaminants, stress responses, virulence and antibiotic resistance. FGAs have been demonstrated as a highly specific, sensitive and quantitative high throughput metagenomic tool for microbial ecology studies and have been widely applied to analyze the functional diversity, composition, structure, function and dynamics of microbial communities from various habitats (e.g., water, soil, sediment, bioreactor). In this chapter, using GeoChip as an example, we will focus on the technical details of the development and evaluation of FGAs, including gene selection, sequence retrieval and verification, probe design and verifications, and computational and experimental evaluation of the specificity, sensitivity and quantification. We also introduce the core functional gene families included in GeoChip. Finally, we will discuss the challenges and future directions for future GeoChip development read more ...