D890 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 1. Phenotype data: new layout, viewing options and tools. An MPD summary plot is shown from an aging study measuring IGF-1 levels in males and females of 33 inbred strains at 6 months of age [Yuan1 (28); see also accompanying paper (29)]. From this plot, users have several choices for viewing (see plot options), and there are one-click options for deploying relevant tools speciﬁc for this measurement (boxed selections just above the plot), which include ﬁnding other phenotype measurements that correlate signiﬁcantly, ﬁnding genes with correlated expression patterns and performing EMMA-corrected genome-wide association analysis (GWAS). For most MPD measurements with at least 20 inbred strains tested, the GWAS option is a direct link to pre-computed results hosted on the UCLA EMMA website (see text). About the plot: strain means are shown (±1 SEM); dotted horizontal lines indicate 1 SD for the overall strain mean (red = female; blue = male). All words in blue are links to tools, other views or additional information. For a continuation of this example, see Figure 2 (GWAS) and Figure 3 (gene expression). and added new or expanded functionality to the MPD Toolbox. Here, we present a comprehensive example to demonstrate the power and utility of MPD and to high- light some of our new tools and features. We start with MPD phenotype data (IGF-1 levels at 6 months of age) and use new MPD tools to conﬁrm and further narrow published mapping results (Yuan1) (28,29). This example spans Figures 1–3 and illustrates the following new or updated features: . Improvement of various tools with new layouts, more options and links to other tools and information (Figure 1). . Development of interfaces to facilitate association mapping using the UCLA EMMA-Correction Server (see below and Figure 2). . Implementation of a user interface for working with gene expression data and providing tools for ﬁnding signiﬁcant correlations to phenotype data using an in- novative variance-based, data-screening feature to minimize false positives (Gene Expression: S12; Correlations Center S14) (Figure 3) and . Implementation of a ‘workbook’ feature to help users pare-down and gather candidate genes with an option to generate an output of gene IDs for quick copy–paste (Figure 3). into other bioinformatics resources MPD has been exploring and evaluating methods for genome-wide association studies (GWAS) that may be developed into general tools for MPD users. One approach that has received a lot of attention is the ‘ef- ﬁcient mixed-model method’ (EMMA), which corrects for inbred strain population structure thereby signiﬁ- cantly reducing the number of false positive associations (30). GWAS results for selected MPD measurements (e.g. testing at least 20 strains) are available in collab- oration with the UCLA Computer Science and Bioinformatics group (ZarLab) using EMMA and the Mouse HapMap for 94 inbred strains at 132K locations (2). Wild-derived strains are automatically excluded from these analyses (see more details in Figure 2). For ineligible MPD measurements (<20 strains), MPD provides an option to produce input-ready ﬁles speciﬁc- ally formatted for a real-time run on the UCLA EMMA Server (mouse.cs.ucla.edu/emmaserver). Users can choose to include wild-derived strains and are able to further manipulate the input ﬁle, e.g. to delete speciﬁc strains, and to select other SNP data sets for interrogation.