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Open Access Highly Accessed Research article

Cell functional enviromics: Unravelling the function of environmental factors

Ana P Teixeira12, João ML Dias3, Nuno Carinhas12, Marcos Sousa2, João J Clemente2, António E Cunha2, Moritz von Stosch3, Paula M Alves12, Manuel JT Carrondo12 and Rui Oliveira13*

Author Affiliations

1 Instituto de Tecnologia Química e Biológica - Universidade Nova de Lisboa (ITQB-UNL), Av. República, Quinta do Marquês, 2781-901 Oeiras, Portugal

2 Instituto de Biologia Experimental e Tecnológica (IBET), Av. República, Quinta do Marquês, 2781-901 Oeiras, Portugal

3 REQUIMTE, Systems Biology & Engineering Group, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT-UNL), 2829-516 Caparica, Portugal

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BMC Systems Biology 2011, 5:92  doi:10.1186/1752-0509-5-92

Published: 6 June 2011

Abstract

Background

While functional genomics, focused on gene functions and gene-gene interactions, has become a very active field of research in molecular biology, equivalent methodologies embracing the environment and gene-environment interactions are relatively less developed. Understanding the function of environmental factors is, however, of paramount importance given the complex, interactive nature of environmental and genetic factors across multiple time scales.

Results

Here, we propose a systems biology framework, where the function of environmental factors is set at its core. We set forth a "reverse" functional analysis approach, whereby cellular functions are reconstructed from the analysis of dynamic envirome data. Our results show these data sets can be mapped to less than 20 core cellular functions in a typical mammalian cell culture, while explaining over 90% of flux data variance. A functional enviromics map can be created, which provides a template for manipulating the environmental factors to induce a desired phenotypic trait.

Conclusion

Our results support the feasibility of cellular function reconstruction guided by the analysis and manipulation of dynamic envirome data.