Software

MarVis: a tool for clustering and visualization of metabolic biomarkers

Alexander Kaever¹ , Thomas Lingner¹ , Kirstin Feussner² , Cornelia Göbel³ , Ivo Feussner³ and Peter Meinicke¹

¹  Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany

²  Department of Developmental Biochemistry, Institute for Biochemistry and Molecular Cell Biology, Georg-August-University Göttingen, Göttingen, Germany

³  Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Göttingen, Germany

author email corresponding author email

BMC Bioinformatics 2009, 10:92doi:10.1186/1471-2105-10-92

Published:	20 March 2009

Abstract

Background

A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as obtained from metabolomic experiments. Intensity-based clustering is an unsupervised approach to the identification of metabolic markers based on the grouping of similar intensity profiles. A major problem of this basic approach is that in general there is no prior information about an adequate number of biologically relevant clusters.

Results

We present the tool MarVis (Marker Visualization) for data mining on intensity-based profiles using one-dimensional self-organizing maps (1D-SOMs). MarVis can import and export customizable CSV (Comma Separated Values) files and provides aggregation and normalization routines for preprocessing of intensity profiles that contain repeated measurements for a number of different experimental conditions. Robust clustering is then achieved by training of an 1D-SOM model, which introduces a similarity-based ordering of the intensity profiles. The ordering allows a convenient visualization of the intensity variations within the data and facilitates an interactive aggregation of clusters into larger blocks. The intensity-based visualization is combined with the presentation of additional data attributes, which can further support the analysis of experimental data.

Conclusion

MarVis is a user-friendly and interactive tool for exploration of complex pattern variation in a large set of experimental intensity profiles. The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.