D1198 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 2. Collage of web interface panels from the PLEXdb implementation of MGI. On the input page (A), users select the source of the genes and the model genome, paste a gene list into the text ﬁeld, select output preferences and submit the query (20). Map (B) and tabular (C) outputs then display genomic positions and provide detailed annotations with links to PlantGDB and Gramene or TAIR. Users may further evaluate the putative orthologs using the gene model display page (D) (21), where they may also specify the output gene model or FLcDNA which can be viewed at PlantGDB. and then apply diverse higher level analyses. The goal is a step-by-step wizard that is easy to use without heavy study and reading of documentation. Gene lists can be created using correlated neighbors of a target gene, fold change under different conditions, common Gene Ontology (GO) terms and pathway mem- bership as shown in Figure 3. Gene lists can also be imported from ofﬂine analysis or an interesting publica- tion. Set operations such as union and intersection can be carried out on the created lists. Once a gene list is created, the user can analyze the list using clustering, ANOVA, etc. A user can set up a group of analyses to perform on the data set. The analysis itself and the results can be stored for registered users. Analyses for guest users are stored for a limited time only. After analysis, the gene list can be annotated and saved in a spreadsheet. Applications of PLEXdb As an example of the utility of PLEXdb, we present a use case. Map all of the expressed genes associated with a particular condition on the genome. An investigator has completed a series of gene expression measurements, performed statis- tical analysis, uploaded the data and has a list of genes associated with a particular treatment. The investigator then wishes to see where all genes that are co-regulated or that belong to a particular gene family map on the