Journal: BMC Genomics
Article Title: A Marfan syndrome gene expression phenotype in cultured skin fibroblasts
doi: 10.1186/1471-2164-8-319
Figure Lengend Snippet: Validation by quantitative qRT-PCR . The figure presents a summary of the 10 genes selected for validation by qRT-PCR. Above each gene name are two "box-and-whisker" plots of expression levels for that gene across 32 unaffected control (UC) samples (left plot of each pair, blue, up-triangles) and 42 MFS affected samples (right, red, down-triangles). Vertical axis is log 10 ratio of expression level to the median UC level. Each "box" shows the inter-quartile range (IQR), i.e., the range between the 25 th and 75 th percentiles of the log ratios; the horizontal line in each box is the 50th percentile (median). (Median log ratio for UC is always zero, by definition.) "Whiskers" (vertical lines) extend from each box to the most extreme values within 1.5 times the IQR from the box; in normally distributed data this would on average encompass 99% of the values. Triangles mark more extreme points. The lower curve shows log 10 (p-value) for a Wilcoxon rank sum test of the null hypothesis that the UC and MFS distribution are identical; horizontal line marks the p = 0.05 significance level. 6 of 10 genes have p-values < 0.05 by this test. Most genes exhibit noticeably greater variability across the MFS samples than across UC samples, although the Wilcoxon test is not sensitive to this. To highlight one example, for Elastin ( ELN ), the middle 50% of the UC sample log ratios fall between -0.23 and +0.14 (i.e., the 25 th and 75 th percentiles of the values fall 1.70-fold below and 1.38-fold above the median, respectively), and all but 4 fall between -0.58 and +0.34 (4-fold below and 2.2-fold above median). In contrast, median Elastin level is 26 fold lower in MFS samples, only four MFS samples are above the UC median, and the null hypothesis has a p-value of 1.6 × 10 -8 .
Article Snippet: Validation of the array results was done using Applied Biosystems pre-designed qRT-PCR primer and probe sets (PDAR's, see ABI P/N 4333458_a.pdf for the complete protocol).
Techniques: Quantitative RT-PCR, Whisker Assay, Expressing
