D1196 Nucleic Acids Research, 2012, Vol. 40, Database issue newly developed nine-plant pathogenic fungal genome array, as well as the full-genome Brachypodium and Maize arrays. PLEXdb also supports the NimbleGen microarray platforms for Vitis and maize (10). All arrays enjoy complete annotation and analysis support. Gene atlas experiments have been specially tagged by the PLEXdb curator to highlight experiments that focus on different plant tissues, developmental stages and im- portant experimental conditions such as biotic and abiotic stress. These experiments allow users to quickly see how their gene of interest behaves under different conditions. The PLEXdb curator reviews the submitted data for overall data quality and looks for signs of common errors such as sample association errors (a sample associated with the wrong data ﬁle) using replicate correl- ation plots. In all cases, the submitter is asked to review the normalized data and is requested to approve the results before posting the data. The curator also regularly reviews GEO for new plant and pathogen array data sets. When high quality new data sets are discovered in GEO (11), the curator determines the experimental factors and imports the data into PLEXdb. GENE ANNOTATION Users can ﬁnd their gene of interest on a speciﬁc expres- sion platform via the PLEXdb tool, Find Your Gene, which blasts sequence against the consensus sequence for each microarray. In addition to linking expression information from ex- periments to probe sets, PLEXdb provides consensus se- quences and annotation for expression elements by linking probe sets to information in several databases, including UniProt, PlantGDB (8) and the Dana Farber Cancer Institute (DFCI) Gene Index (12). It also associates probe set IDs with annotation data from other sources, such as organism-speciﬁc consortiums such as Gramene (13), TAIR (14), MaizeGDB (15) and the Fusarium graminearum Database (FGDB) (16). When model genomes are available, annotations and links to alignment tools (e.g. Model Genome Interrogator) are provided. Links to appropriate clade- or organism-speciﬁc databases are made (e.g. Gramene for gene models for rice, GrainGenes for physical maps of wheat). The connections to other databases are in most cases determined through BLAST (BLASTN, BLASTX, or TBLASTX). Links to PlantGDB-assembled unique transcripts (PUT) assemblies are also provided for every applicable GeneChip (8). The expression elements are also linked to gene ontology terms via the UniPROT links. Links to metabol- ic pathway information allow users to know what pathway their genes are in. Various pipelines exist for the data behind the microarray annotation. For example, the PLEX team runs different types of BLAST and BLASTX against a variety of references bi-annually. The results are stored and used for updating GO and PO tables. These pipelines are all implemented in Perl. EXPERIMENT ANNOTATION AND PROCESSING PLEXdb uses the MIAME/Plant (7) guidelines to provide as complete a description of each experiment as possible. Wherever possible, strict structures and controlled vocabularies are used. Of primary importance to enable quick understanding and to facilitate machine- searchable experiments is the use of a factor/level de- scription of the experiment treatment structure. PLEXExpress, the submission tool is used to enable MIAME compliance and use of controlled vocabularies (17). Submitters are also encouraged to include images in their submissions. PLEXdb uses a factorial design structure that allows for easy comparison between conditions. A factor is a condi- tion that is changed between samples. For example, a factor may be the genotype, type of pathogen inoculation, stress condition, or time point. A level is a speciﬁc change in a factor. For example, an experiment might test differ- ences between genotypes A and B. In this case, the factor is ‘genotype’ and its levels are ‘A’ and ‘B’. Wherever possible, PLEXdb uses the Plant Ontology (18) (PO) terms for development stages, cell types, organism parts and other controlled term lists. Many of these lists come from the MIAME/plant requirements (7); e.g. the terms for describing growth media. This helps pave the way toward comparative expression data analysis and meaningful meta-analyses. The experiments submitted to PLEXdb may be kept private to the submitter, shared with a group of collabor- ators only, or made visible to the public. This enables re- searchers to use PLEXdb as a collaborative tool while a study is ongoing. An experiment submitter can also request a reviewer access code so that reviewers can look at the data from an experiment while evaluating a paper. In accordance with journal policies, upon publi- cation of the primary manuscript, data is considered public. PLEXdb requires submitted experiments to provide, at a minimum, the raw data ﬁles and sample and protocol information. Other ﬁle types are optional and all submitted ﬁles are available for public downloading when the experiment is made visible to the public. If the researcher requests it, PLEXdb submits the formatted ex- periments and meta-data to GEO in the name of the re- searcher and his/her lab. For each experiment, all ﬁles provided by the submitter are made available for download according to the visibility of the experiment (private, group or public). In addition, PLEXdb provides the normalized data, tables of treatment means and medians and a tab-separated text ﬁle correlating CEL ﬁles to treatments and replicates. After an experiment has been submitted and reviewed by the curator for completeness and correctness, the raw data is normalized by using the Robust Multichip Average (RMA) (19) method and by the Affymetrix MAS5.0 nor- malization. Several visualizations are generated, including RNA degradation, box plots of raw and normalized intensities by all treatments across the experiment, treat- ment clustering across the experiment, various treatment scatter plots. This pipeline was constructed using Perl, R,