Integration of bioinformatics tools in candidate gene prioritization of co-regulated gene sets in Saccharomyces cerevisiae
© Abedi et al; licensee BioMed Central Ltd. 2011
Published: 5 August 2011
The availability of massive amounts of heterogeneous and distributed biological data has prompted the development of a wide range of data analysis and data mining tools in the area of bioinformatics. However, due to the nature of the biological data, performing a specific analysis by combining such tools can be complicated and cumbersome. Yet, integration of number of tools can provide complementary information, and improve the efficiency of the data analysis to further our understanding and knowledge discovery. The development of an integrated software platform can considerably enhance the usability of such tools and benefits the research communities at large. Towards that goal, this study focuses on systematically integrating a number of tools for analyzing Saccharomyces cerevisiae data in order to improve candidate gene prioritization from microarray data using evidences from complementary sources.
Microarray data from a recent study by Ouyang et. al. was used to evaluate the proposed framework. An array of free and open source bioinformatics tools were used to develop the Saccharomyces Integrated Software Platform (SISP). In particular, sources of information used in this analysis include literature data, Gene Ontology, physical and genetic interaction data as well as pathway information. SISP has the strength of combining prior knowledge with user-defined weighting of different sources of evidence. Access to the integrated tool will be facilitated by a user-friendly web interface with options including data query, import, export, analysis and visualization.
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.