A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices

Abstract

Escherichia coli is a versatile organism that can grow at a wide range of oxygen levels; although heavily studied, no comprehensive knowledge of physiological changes at different oxygen levels is known. Transcriptomic studies have previously examined gene regulation in E. coli grown at different oxygen levels, and during transitions such as from an anaerobic to aerobic environment, but have tended to analyse data in a user intensive manner to identify regulons, pathways and relevant literature. This study looks at gene regulation during an aerobic to anaerobic transition, which has not previously been investigated. We propose a data-driven methodology that identifies the known pathways and regulons present in a set of differentially expressed genes from a transcriptomic study; these pathways are subsequently used to obtain a corpus of published abstracts (from the PubMed database) relating to each biological pathway.