Top 25 differentially expressed Affymetrix probes are shown in Table 1 (complete list is shown in Table S1, statistically summary is shown in Table S2).
Thus, the experimental dataset was obtained by assessing the gene expression levels of the 20 genes by real time PCR in a cohort of 104 subjects, composed by healthy controls and patients with MS (see Table 1 for details of the clinical characteristics and Table S1 for statistically summary of gene expression levels).
Overall, 30 (63%) of the 48 meta-analyses of observational studies reported a nominally statistically significant summary result (tables 1 and 2). Figure 3 shows a forest plot with the summary effects of all the non-overlapping meta-analyses of observational studies (for binary outcomes).
Many statistically consistent summary methods have been developed for estimating species trees when gene discordance is due to ILS [ 13- 19].
To examine the role of coexpressed genes, functional enrichment tests can provide a statistically based summary of functional terms that occur more often than chance in a gene test set.
In this study, we address the following questions: 1 How does SVDquartets+PAUP* compare to ASTRAL-2 and NJst, two of the best performing statistically consistent summary methods? 2 How do the statistically consistent methods we study compare to a concatenated analysis using maximum likelihood? 3 How do all the methods perform on short sequences?
Of the 48 meta-analyses, 18 (38%) had nominally statistically significant summary associations according to random effects calculations and had no evidence of small study effects (P≥0.10), not very large heterogeneity (I≤75%), and no evidence for excess significance (tables 1 and 2).
However, meta-analyses of randomised controlled trials reported a nominally statistically significant summary result for only 13 of the 57 outcomes, and the confidence intervals of the estimates were generally wider than the confidence intervals of the meta-analyses of observational studies.
PADE analysis provides statistically valid summary measures including false discovery rates along with transcript sets that are typically much more useful and indicative of differential expression between groups than using techniques such as p-values alone, corrected p-values, or p-values with fold change estimates.
The meta-analysis, using a random effects model, produced a statistically significant summary effect measure of 17% excess risk (95% CI, 2 34) [(Table 2, Figure 1; see also Supplemental Material 1, Table 1, available online (doi 10.1289/ehp. 0900677.S1 via http://dx.doi.org/)].
Although the study yielded a statistically significant interaction summary statistic (P interaction= 0.005), which was directionally consistent with the original studies' findings (22), the effect estimate was heterogeneous (I = 36%), suggesting the presence of one or more latent effect-modifiers (i.e., unidentified factors that change the magnitude of FTO's effect on BMI).
