PLEXdb is an interactive gene expression resource for plants and plant pathogens. PLEXdb provides annotation, visualization, and integration of data and tools that allow users to perform complex analyses quickly and easily. PLEXdb has added support for the NimbleGen arrays for grape and maize as well as supporting the new Maize gene atlas. The Model Genome Interrogator (MGI) tool supports aligning gene lists onto corresponding genes from model plant organisms, rice and Arabidopsis, identifying putative orthologs in the process. MGI allows researchers to view annotations, visually evaluate gene models and extract sequence data from promoters, exons, introns and UTRs. PLEXdb also provides methods for users to track how gene expression changes across many different experiments using the Coefficient of Variation (CV) based data mining tools. Gene OscilloScope finds data sets and treatments that affect the level of fluctuation of expression of a gene of interest. A new related tool with the reverse functionality, Fluctuation Filter, can find genes which are influenced by the treatments in any data set of interest. Fluctuation Filter also can be used to find a gene’s suitability as a steady-state control. The gene list-processing wizard guides users through PLEXdb functions for creating, analyzing, annotating and managing gene lists. Users can upload their own lists or create them from the output of PLEXdb tools, and then apply diverse higher-level analyses, such as ANOVA and clustering. The operational scope of these utilities now has reached data from more than 11,600 gene chips corresponding to 470 data-sets.