Nucleic Acids Research, 2012, Vol. 40, Database issue D1195 Figure 1. Interconnection between PLEXdb and a few of its partner databases. Utilizing the PLEXdb annotation portal, every transcript (for every PLEXdb organism) will be presented as an expression proﬁle (upper right), linked to analytical functions (Gene OcilloScope, MPT, MGI, etc.), and aligned on species-speciﬁc genome browsers to sequenced and model genomes (e.g., maize, soybean Brachypodium, grape, etc.), providing one-stop- shopping for the plant genome community. data available to public users, but because of their large scope and lack of speciﬁcity they do not provide commu- nity annotation. The most useful expression databases for on-line analysis and data exploration tend to focus on particular species or problems as they contain links to useful anno- tation as well as graphics and tools focused at a par- ticular task. Examples of these databases include GENEVESTIGATOR (5) and the Sol Genomics Network (SGN) (6). GENEVESTIGATOR has an exten- sive set of on-line tools for analysis and visualization of Arabidopsis and other model species microarray data, with searches based on tissue type and developmental stage, but it lacks annotation links and does not allow public sub- mission or download of data. SGN provides a uniﬁed resource with sequence, expression and pathway data but it is restricted to a single clade. DESIGN REQUIREMENTS AND FUNCTIONALITY The key design requirements for PLEXdb are to allow users to explore data sets and put them into biological context for interpretation. This requires that the database contains carefully annotated and curated experi- ments with links to controlled vocabularies so that appro- priate comparisons can be made for experiments. Gene expression elements must also be thoroughly documented and annotated with timely information. Careful comparisons across species and mapping onto key model organisms allow biologist users to use existing structures to enhance their analyses. Finally, the database must be easy to use and the data should be presented in a form amenable to interpretation. To meet these goals, the PLEXdb team: . Encourages users to submit fully annotated experi- ments to PLEXdb which meet/exceed the MIAME/ Plant requirements (7). . Provides up-to-date annotation of probe sets from a variety of sources such as clade-speciﬁc databases, RefSeq, UniPROT and PlantGDB (8). . Creates visualizations that allow users to quickly explore experiment quality and consistency prior to using data in their analyses. . Provides analysis tools such as the Gene List Suite which steps users through the analysis process of creating, analyzing, annotating and managing a gene list. PLEXdb content PLEXdb supports all of the available plant and pathogen GeneChip arrays including, Affymetrix 57K Rice, 61K Wheat, 22K Barley1, 18K ﬁrst-generation Maize, 8K Sugarcane, Fusarium graminearum (9), 61K Soybean/ Phytopthora/soybean cyst nematode, 16K Grape, Arabidopsis ATH1 as well as Cotton, Poplar, Citrus, Tomato and Medicago.Recent additions include the