Connectivity map data and associated methodologies have become a valuable tool in understanding drug mechanism of action (MOA) and discovering new indications for drugs. However, few systematic evaluations have been done to assess the accuracy of these methodologies. One of the difficulties has been the lack of benchmarking data sets. Iskar et al. (PLoS. Comput. Biol. 6, 2010) predicted the Anatomical Therapeutic Chemical (ATC) drug classification based on drug-induced gene expression profile similarity (DIPS), and quantified the accuracy of their method by computing the area under the curve (AUC) of the Receiver Operating Characteristic (ROC) curve. We adopt the same data and extend the methodology, by using a simpler eXtreme cosine (XCos) method, and find it does better in this limited setting than the Kolmogorov-Smirnov (KS) statistic. In fact, for partial AUC (a more relevant statistic for actual application to repositioning) XCos does 17% better than the DIPS method (p=1.2e-7). We also observe that smaller gene signatures (with 100 probes) do better than larger ones (with 500 probes), and that DMSO controls from within the same batch obviate the need for mean centering. As expected there is heterogeneity in the prediction accuracy amongst the various ATC codes. We find that good transcriptional response to drug treatment appears necessary but not sufficient to achieve high AUCs. Certain ATC codes, such as those corresponding to corticosteroids, had much higher AUCs possibly due to strong transcriptional responses and consistency in MOA.
