Comparing null hypotheses. Comparison of p-values obtained by sample label permutations and gene permutations, using the data set of van 't Veer et al.  (left), Golub et al.  (middle), and Alon et al.  (right). Sample label permutation results were obtained with 100.000 permutations for the van 't Veer et al. data set and with 10.000 permutations for the other data sets. Gene permutation results were calculated as described in Methods. Red, green and blue colours represent categories with 1 to 5, 6 to 20, and over 20 genes, respectively. Encircled boxes in the left figure represent the categories "M phase" and "carboxylic acid metabolism", which are further discussed in the text.