Bioinformatics strategies for the analysis of lipids

Owing to their importance in cellular physiology and pathology as well as to recent technological advances, the study of lipids has reemerged as a major research target. However, the structural diversity of lipids presents a number of analytical and informatics challenges. The field of lipidomics is a new postgenome discipline that aims to develop comprehensive methods for lipid analysis, necessitating concomitant developments in bioinformatics. The evolving research paradigm requires that new bioinformatics approaches accommodate genomic as well as high-level perspectives, integrating genome, protein, chemical and network information. The incorporation of lipidomics information into these data structures will provide mechanistic understanding of lipid functions and interactions in the context of cellular and organismal physiology. Accordingly, it is vital that specific bioinformatics methods be developed to analyze the wealth of lipid data being acquired. Herein, we present an overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and application of its tools to the analysis of lipid data. We also describe a series of software tools and databases (KGML-ED, VANTED, MZmine, and LipidDB) that can be used for the processing of lipidomics data and biochemical pathway reconstruction, an important next step in the development of the lipidomics field.