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Open Access Highly Accessed Methodology article

h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data

Yvonne E Pittelkow and Susan R Wilson

Author Affiliations

Mathematical Sciences Institute, Australian National University, Building 27, Canberra, ACT 0200, Australia

BMC Bioinformatics 2007, 8:486  doi:10.1186/1471-2105-8-486

Published: 20 December 2007

Abstract

Background

An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid this process, potentially contributing to the identification of co-regulated genes and gene function as well as network development.

Results

We introduce the h-Profile plot to display gene expression profiles. Thumbnail versions of plots of gene expression profiles are plotted at coordinates such that profiles of similar shape are located in the same sector, with decreasing variance towards the origin. Negatively correlated profiles can easily be identified. A new method for selecting genes with fixed periodicity, but different phase and amplitude is described and used to demonstrate the use of the plots on cell cycle data.

Conclusion

Visualization tools for gene expression data are important and h-profile plots provide a timely contribution to the field. They allow the simultaneous visualization of many gene expression profiles and can be used for the identification of genes with similar or reversed profiles, the foundation step in many analyses.