D892 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 3. New gene expression interface. Continuing with the IGF-1 example [Yuan1 (28)] from Figures 1 and 2, we interrogated the Chr 10 QTL interval (84.5–90.0 Mbp) identiﬁed by both association mapping methods (HAM and EMMA) using the new MPD gene expression interface. Users can simply click on the correlated probes/genes option above the plot shown in Figure 1 (the relevant part of this panel is shown in the upper-left panel for convenience), or users may choose to begin in the Correlations Center (S14). Of those 21 candidate genes identiﬁed by Leduc et al. (29) (see Figure 2), we went on to conﬁrm that 6 of those genes had compelling expression proﬁles consistent with IGF-1 levels (P < 0.05). Three of these genes are listed in the middle-left panel (see Note 1 for more information about this panel). As indicated, three probesets from two gene expression projects [GX-Su1 (31,32), GX-Tabakoff1 (33)] were identiﬁed using various ﬁltering and sorting options that are available with this tool. Users can adjust stringency to broaden or narrow results by selecting P-value cutoff and setting the data point variance (DPV) quality ﬁlter where stricter settings will omit probesets that have larger standard errors relative to the range of strain means. Users may further ﬁlter results by minimum number of strains, sex, speciﬁc data set and chromosome. Results can be sorted by P-value, correlation coefﬁcient, location order, MPD project or MPD category. A phenotype-gene expression scatterplot is available through the ‘Plot’ link. IGF-1 versus Nr1h4 for males is shown in the lower-left panel. By clicking on gene name, we accessed the gene directory page (lower-right panel, and see Note 2 below), to deploy the 550K SNP panel [CGD2 (3,6)] speciﬁcally for the gene of interest to compare the segregation of phenotype with polymorphisms. Using MPD SNP tools, we conﬁrmed that three of the six genes have polymorphic intronic or UTR regions, consistent with the notion that these genes are differentially regulated. The corresponding SNP results for Nr1h4 are shown (middle-right panel) where strains are grouped according to ‘hi’ (left) or ‘lo’ (right) IGF-1 levels. These strains fall into two major haplotypes (wild-derived strains fall into a third haplotype, not shown). For ease of comparison, an optional view of the male IGF-1 data is shown in the upper-right panel [color-guides from the SNP results to plot: blue = high IGF-1 levels, yellow = low IGF-1 levels (see also, strain distribution in Figure 1)]. All words in blue are links to tools, other views or additional information. While we demonstrate that MPD can help identify (or further verify) candidate genes exhibiting differential expression, we also note that caution should be used in making claims of causality based solely on microarray data, SNPs and functional relevance of positional candidates. All MPD phenotype-gene expression pair-wise correlations are available for bulk download (Download Center: S16). Note 1: The ‘collect gene’ option in the middle of the gene expression (continued)