INVESTIGADORES
CARRARI Fernando Oscar
artículos
Título:
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
Autor/es:
MILONE, D; STEGMAYER, G; KAMENETZKY, L; LÓPEZ, M; LEE, JM; GIOVANNONI, JJ; CARRARI, F
Revista:
BMC BIOINFORMATICS
Editorial:
BIOMED CENTRAL LTD
Referencias:
Año: 2010 vol. 11 p. 1 - 10
ISSN:
1471-2105
Resumen:
Background: Modern biology uses experimental systems that involve the exploration of phenotypic variation as aresult of the recombination of several genomes. Such systems are useful to investigate the functional evolution ofmetabolic networks. One such approach is the analysis of transcript and metabolite profiles. These kinds of studiesgenerate a large amount of data, which require dedicated computational tools for their analysis.Results: This paper presents a novel software named *omeSOM (transcript/metabol-ome Self Organizing Map) thatimplements a neural model for biological data clustering and visualization. It allows the discovery of relationshipsbetween changes in transcripts and metabolites of crop plants harboring introgressed exotic alleles andfurthermore, its use can be extended to other type of omics data. The software is focused on the easyidentification of groups including different molecular entities, independently of the number of clusters formed. The*omeSOM software provides easy-to-visualize interfaces for the identification of coordinated variations in the co-expressed genes and co-accumulated metabolites. Additionally, this information is linked to the most widely usedgene annotation and metabolic pathway databases.Conclusions: *omeSOM is a software designed to give support to the data mining task of metabolic andtranscriptional datasets derived from different databases. It provides a user-friendly interface and offers severalvisualization features, easy to understand by non-expert users. Therefore, *omeSOM provides support for datamining tasks and it is applicable to basic research as well as applied breeding programs. The software and asample dataset are available free of charge at http://sourcesinc.sourceforge.net/omesom/
