Table 2, which found significant support for some pathways.46,56 One of the major drawbacks of gene-set analyses is that they require predefined sets of genes. Gene sets defined by current annotation databases, such as KEGG or GO, vary in their completeness; some pathways are more complete than others. Moreover, databases also vary in how they define gene sets. Thus, a given gene may belong to one pathway in one database and a second pathway in another. Although these challenges are not unsubstantial, we think greater use of pathway-type analyses is needed.
