Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments

摘要

The proportion of equivalently changed pathways detected by each method, when the probability of equivalent change was 0.5. The x-axis displays the symmetry, which shows the probability of genes being up-regulated in the pathway as opposed to down-regulated (when they were differentially expressed). With a symmetry of 0.5, approximately half of the differentially expressed genes would be up-regulated and the rest would be down-regulated. The different lines show the sensitivity for different levels of probability of a gene being differentially expressed. The results are shown for (A) ECEA, (B) GSEA, and (C) ORA. For nearly all levels of probability of differential expression, ECEA was more sensitive than ORA. ECEA was also more sensitive than GSEA whenever the genes were not highly co-expressed (symmetry near .1 or .9)