Urzúa et al. BMC Genomics 2010, 11(Suppl 5):S1 http://www.biomedcentral.com/1471-2164/11/S5/S1 Page 3 of 11 Figure 1 Consistency of microarray results and Q-PCR confirmation of selected genes Normalized microarray data of 5 cDNA clones of Tsc22 (A), 4 clones of Col3a1 (B) and 4 clones of Fubp1 (C) were compared between samples s1 and s2 (corresponding to 2 of the 4 mouse ovarian samples assayed) across 6 microarray replicates each. Adjusted p-values and expression change (ec), defined as the difference between log2 averages are shown. In D, the coordinates of scatter plot depicts the average of normalized microarray ratios (5-6 replicates) and the average of duplicate Q-PCR assays for the genes Spp1, Txnrd1, Anxa5, Fn1, C1s, Ctsl, and Mt1 in each of the 4 mouse strains. The internal control transcript was the 18S rRNA. Q-PCR data was converted to log2 scale ratios as described in Methods. The squared correlation coefficient (R2) shown corresponds to the overall gene subset in the 4 strains (i.e. 28 data pairs). Raw Q-PCR results and individual microarray ratios are detailed in Additional file1, table 1. across strains. Thus, in order to add physiological mean- ing to this observation, the whole microarray dataset was subjected to a linear regression analysis with each of the continuous covariates shown in Table 1. A sum- mary of regression results is shown in Table 2. Using an adjusted p value <0.05 as cut-off, a total of 590 clones that represented 401 known genes, 93 unknown genes, 45 transcribed locus and 9 expressed sequences were significantly correlated to 4 of the 5 traits analyzed. The overlap between the regression analysis and the ANOVA test was 386 clones. The phenotype productive matings (PM) did not result in any significantly Table 1 Ovarian tumor and reproductive phenotypes in selected mouse strains Strain Tumor frequencya Litter sizeb Number of litters Productive matings (%) BALB/c 3.80 4.9 3.6 55.6 C57BL/6 1.60 6.6 3.8 87.4 FVBc 7.00 9.5 4.8 90.0 SWR 57.0 7.5 2.3 58.3 Relative fecundity 9.80 21.9 41.0 10.1 a Refers to spontaneously arisen tumors in inbred mice. Data corresponds to the “highest reported tumor frequency” in all literature records collected in the Mouse Tumor Biology Database [9], (http://tumor.informatics.jax.org/mtbwi/dynamicGrid.do;jessession=89370725979E9B939D3DD40AB4961BA5) for each strain/ organ combination where organ=ovary. b Litter size, number of litters, and productive matings were taken from the Mouse Phenome Database [8] (http://www.jax.org/phenome). Data acquisition, curation and handling are described at http://phenome.jax.org/db/q?rtn=docs/aboutmpd. The parameter “relative fecundity” is derived form the other 3 reproductive parameters [5]. c Data of FVB strain was taken from Silver’s Mouse Genetics textbook [5].