Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets

Abstract

Coexpression patterns of gene expression across many microarray data sets may reveal networks of genes involved in linked processes. To identify factors involved in cellulose biosynthesis, we used a regression method to analyze 408 publicly available Affymetrix Arabidopsis microarrays. Expression of genes previously implicated in cellulose synthesis, as well as several uncharacterized genes, was highly coregulated with expression of cellulose synthase (CESA) genes. Four candidate genes, which were coexpressed with CESA genes implicated in secondary cell wall synthesis, were investigated by mutant analysis. Two mutants exhibited irregular xylem phenotypes similar to those observed in mutants with defects in secondary cellulose synthesis and were designated irx8 and irx13. Thus, the general approach developed here is useful for identification of elements of multicomponent processes.

Fig. 1.

Venn diagrams show overlapping coexpressed genes for the 100 highest ranked genes with the individual CESA genes for the primary (A) and secondary (B) CESA complexes.

Fig. 2.

Cross sections of stem vascular bundles. Stem sections were stained with toluidine blue O and viewed under a compound microscope. (A) WT. (B) irx1. (C) irx8. (D) irx13. Arrows indicate deformed xylem elements.