Tools for Meta-Analysis

Function-prediction tools using meta-analysis of microarray data are available from http://digbio.missouri.edu/meta_analyses/. All programs were written using ANSI C language, and they are compatible with both Linux, as well as Windows, operating systems.

5.9 Conclusion

This chapter introduced various aspects of GO and its applications in gene function and regulatory-network characterization. GO provides a controlled vocabulary to map functions of genes into identifi ers in any organism. This notation makes the computational method feasible to manipulate gene functions in terms of ontology or certain types of mapping. GO tremendously saved the time for other researchers to collect up-to-date function annotation from the literature, as it is continuously updated, and new versions are made available on a monthly basis. There are also

some other types of ontologies, such as the KEGG ontology. KEGG (Kyoto Ency-clopedia of Genes and Genomes) is a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. More ontologies are in-troduced in Chapter 1 of this book.

GO offers the most comprehensive sets of relationships to describe gene/pro-tein activities. However, GO also has some limitations. For example, some GO terms are generic and not informative for biological studies, although GO has been improved with more specifi c function details over the years. Furthermore, GO’s choice to segregate gene ontology to subdomains of molecular function, biologi-cal process, and cellular component creates some limitations [55]. With further developments of gene ontology to overcome these limitations, new computational methods for gene-function prediction will also emerge.

Acknowledgements

We would like to thank our collaborators, Drs. R. Michael Roberts and Jeffery Becker. We would also like to thank Yu Chen for his early involvement in this work.

This study was supported by USDA/CSREES-2004-25604-14708 and NSF/ITR-IIS-0407204 and a Monsanto internship for Gyan Srivastava.

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Mapping Genes to Biological Pathways