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

Date

2007-12-20

Authors

Pittelkow, Yvonne
Wilson, Susan R

Journal Title

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Volume Title

Publisher

BioMed Central

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.

Description

Keywords

Keywords: Cell cycle; Co-regulated genes; Gene Expression Data; Gene expression profiles; Gene function; Network development; Time course datum; Visualization tools; Gene expression; Visualization; Data visualization; article; cell cycle regulation; computer progra

Citation

BMC Bioinformatics 8.486 (2007)

Source

BMC Bioinformatics

Type

Journal article

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DOI

10.1186/1471-2105-8-486

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