CarGene: Characterization of Sets of Genes based on Metabolic Pathways Analysis
Jesus S. Aguilar-Ruizab, Domingo S. Rodriguez-Baenaab,
ABSTRACT
The great amount of biological information stored in public databases provides scientists with an incomparable framework for verifying and testing the results of new algorithms. The integration of huge databases with searching techniques in order to automatically validate results from different sources is a key factor in bioinformatics. Several tools have been developed for analyzing gene-enrichment in terms. Most of them are Gene Ontology{based tools, i.e. these analyze gene-enrichment in GO annotations.
In this work, we introduce a software tool, named CarGene (Charac- terization of Genes), that helps scientists to validate sets of genes by us- ing the biological knowledge on metabolic pathways stored in the Kyoto Encyclopedia of Genes and Genomes (Kegg), and providing a friendly graphical environment to analyze and compare results generated by dif- ferent clustering and/or biclustering techniques. CarGene is based on the degree of coherence of genes in (bi)clusters with respect to metabolic pathways of organisms stored in Kegg, and provides an estimate of obtaining results by chance, including two statistical corrections (Bon- ferroni, and Westfall and Young). One of the most important features of CarGene is the possibility of simultaneously comparing and statis- tically analyzing the information about many groups of genes in both visual and textual manner. Furthermore, it includes its own web browser to explore in detail the information extracted from Kegg. To show the functionality of CarGene, a test based on the study carried out by Huttenshower et al. is performed.
CarGene is intended to be an useful tool for rapidly characterizing the results of diferent clustering or biclustering techniques over the same gene expression dataset. CarGene is freely available in the following web link: http://www.upo.es/eps/bigs/cargene.html.
Contact:
bigs@upo.es |
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