(A) and (B). Sequential comparisons of tissue samples with highest vs. lowest OXPHOS expression. In five large microarray datasets (≥ 180 samples each; GSE5406 myocardium, GSE10780 breast tissue, GSE11223 colon, GSE11375 blood mononuclear cells, GEO13507 bladder tissue, Additional File 2), samples were first ranked according to the average expression of all genes belonging to the KEGG pathways of oxidative phosphorylation (OXPHOS). Then, gene expression was compared between group of samples containing between 10 and 13 tissue samples (depending on the size of the dataset) with the highest and lowest OXPHOS expression, the second-highest and second-lowest OXPHOS expression, and so on, using Significance Analysis of Microarrays (SAM) with a false discovery rate (FDR) of 5%. The largest differences were observed for the samples with the highest and lowest OXPHOS gene expression (comparison "1"). For the remaining comparisons (numbered "2"-"10"), the number of differentially expressed transcripts declined rapidly and was zero for samples showing only minor differences in OXPHOS expression levels (comparisons "8"-"10"). Panel B shows the mean ± SEM of all five datasets.
Barth et al. BMC Genomics 2010 11:197 doi:10.1186/1471-2164-11-197