One of the challenges of functional genomics is to create a better understanding of the biological system being studied so that the data produced are leveraged to provide gains for agriculture, human health and the environment, according to F.M. McCarthy and E. Lyons of the University of Arizona.

Their paper, presented at a symposium at the University of Georgia in 2012 and published in full in Poultry Science recently, explains that functional modelling enables researchers to make sense of these data as it re-frames a long list of genes or gene products (mRNA, ncRNA and proteins) by grouping based upon function, be it individual molecular functions or interactions between these molecules or broader biological processes, including metabolic and signaling pathways.

However, they continue, poultry researchers have been hampered by a lack of functional annotation data, tools and training to use these data and tools. Moreover, this lack is becoming more critical as new sequencing technologies enable us to generate data not only for an increasingly diverse range of species but also individual genomes and populations of individuals.

McCarthy and Lyons discuss the impact of these new sequencing technologies on poultry research, with a specific focus on what functional modelling resources are available for poultry researchers.

They also describe key strategies for researchers who wish to functionally model their own data, providing background information about functional modeling approaches, the data and tools to support these approaches, and the strengths and limitations of each. Specifically, they describe methods for functional analysis using Gene Ontology (GO) functional summaries, functional enrichment analysis, and pathways and network modeling.

As annotation efforts begin to provide the fundamental data that underpin poultry functional modelling (such as improved gene identification, standardised gene nomenclature, temporal and spatial expression data and gene product function), tool developers are incorporating these data into new and existing tools that are used for functional modeling, and cyber-infrastructure is being developed to provide the necessary extendibility and scalability for storing and analysing these data.

This process will support the efforts of poultry researchers to make sense of their functional genomics data sets, say the Tuscon-based researchers, and they provide a starting point for researchers who wish to take advantage of these tools.

This paper was presented as part of the Experimental Design for Poultry Production and Genomics Research Symposium at the Poultry Science Association’s annual meeting in Athens, Georgia in July 2012.

Reference

^{McCarthy F.M. and E. Lyons. 2013. From data to function: Functional modeling of poultry genomics data. Poult. Sci. 92(9):2519-25291. doi: 10.3382/ps.2012-02808}

October 2013