Nucleic Acids Research, 2012, Vol. 40, Database issue D1199 Figure 3. Collage of web interface panels from the PLEXdb Gene List Suite. On the input page (A), users select what they would like to do. (B)shows the inputs and outputs for creating a gene list by selecting proﬁle neighbors. Users may further evaluate the gene list using the Analysis page (C), where they may select multiple analysis steps to be used for the gene list. (D) shows the results of hierarchically clustering the gene list of proﬁle neighbors using BB4 data sets. genome. This is particularly useful for investigators inter- ested in high-throughput quantitative trait (QTL) analysis. For fully annotated sequenced genomes, such as rice or Arabidopsis, Medicago, soybean, poplar and maize, this will be possible by a straightforward look-up of the pre-calculated coordinates in a genome browser. However, the problem is more complex for species without fully sequenced genomes, for example wheat or barley. In this case, it is desirable to identify syntenic pos- itions on the most closely related model genome. These map locations could then be used to search for associ- ations with trait loci to integrate gene expression data with phenotype data. The investigator may also be inter- ested in which gene families and pathways (GO or IUPAC terms) are implicated in the list of co-regulated genes. The investigator may then want to see conserved genes or pathways in another organism (e.g. Arabidopsis) to build hypotheses regarding function by transitive inference and comparison of expression proﬁles of similar experiments in the other organism. The integration of data sources, visualizations and analytic tools at PLEXdb facilitate this process. For example, as shown in Figure 2, the Model Genome Interrogator can perform batch mapping of expression