Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds

Background: Gene expression studies increasingly compare expression responses between different experimental backgrounds (genetic, physiological, or phylogenetic). By focusing on dynamic responses rather than a direct comparison of static expression levels, this type of study allows a finer dissection of primary and secondary regulatory effects in the various backgrounds. Usually, results of such experiments are presented in the form of Venn diagrams, which are intuitive and visually appealing, but lack a statistical foundation. Results: Here we introduce Vector Analysis (VA) as a simple, yet principled, approach to comparing expression responses in different experimental backgrounds. VA enables the automatic assignment of genes to response prototypes and provides statistical significance estimates to eliminate spurious response patterns. The application of VA to a real dataset, comparing nutrient starvation responses in wild type and mutant Arabidopsis plants, reveals that consistent...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Rainer Breitling, Patrick Armengaud, Anna Amtmann
• Keywords: BMCBI 2005, Expression Responses, Gene Expression, Static Expression Levels