Table 2 The number of enriched Go-categories are counted over all 24 clusters at a false discovery rate of 0.05 which is the default configuration of GoMiner. k-means and PCA+k-means do not show any eye specific enrichement in any of the clusters. Only LE+k-means provides one cluster that is enriched for 3 categories specific to eye development. These categories would have even been picked at an FDR of 0.01 suggesting strong statistical support for the LE+k-means performance. Potential nonlinear structures in the data could be an explanation for this observation, see Figure 13.

From: Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development