has specified data input has specified data output implements has format specification is published by is executed in Kolmogorov Smirnov rank-sum based algorithm Gene list R data frame topGO http://bioconductor.org/packages/2.4/bioc/html/topGO.html Nandini Badarinarayan topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. BioConductor Software R software differential expression analysis Bioconductor