Reciprocal Rank-Based Comparison of Ordered Gene Lists

There is growing interest in using rank-ordered gene lists to avoid excessive dependence on measured gene expression levels, which can vary strongly across experiments, platforms, or analysis methods. As a useful tool for working with these lists, this paper describes two extensions of an ordered list comparison measure, recently proposed for comparing Internet search engines: the use of random permutations to assess the significance of differences between ordered lists, and a graphical extension that highlights the items responsible for the main differences between two lists. The method is illustrated for a prostate cancer example from the genomics literature.