Figure 3.

A Comparison of LeFE with PathwayRF Shown is a comparison of Learner of Functional Enrichment (LeFE) and PathwayRF with respect to the size distribution of categories identified as important for breast cancer classification using the Gene Ontology (GO) biological process categories. (a) Scatter plots showing category rank versus category size. Ties in category ranks were resolved through random reordering. Red lines are lowess regressions. (b) Comparison of GO superset and subset ranks. Almost all points for PathwayRF are below the blue x = y line, indicating that supersets rank lower (better) than that their corresponding subsets. The panel for LeFE shows no such bias. (c) The GO biological process hierarchy (with the most general categories toward the top). Blue circles denote the top 25 categories ranked by PathwayRF; red circles denote the same for LeFE; and yellow circles denote categories in the top 25 for both algorithms. The mean GO level is 4.92 for PathwayRF and 7.08 for LeFE. There are no cases in which LeFE's top results are the ancestors of top results from PathwayRF. However, the black edges highlight eight cases in which LeFE found categories that are progeny of categories identified by PathwayRF.