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Table 2 Comparison of different cutoff independent approaches. The top ten categories and their corresponding ranks for each of the the four methods: Wilcoxon rank sum (WRS) with sample label permutation null hypothesis (s.l.p.), WRS with gene permutation null hypothesis (g.p.), the Kolmogorov-Smirnov score (K-S) as used in GSEA [17], and the minimal cutoff-based p-value (min-p) [7, 8]. Percentile columns indicate the position of the 25th, 50th and 75th percentile in the ranked gene list which comprises 5224 genes and is based on the data set of van't Veer et al.. The last column indicates the number of genes in each category. The full table is available as a supplementary file [see Additional file 3].

From: Comparing functional annotation analyses with Catmap

GoName GoId WRS K-S min-p 25% 50% 75% #genes
   s.l.p. g.p.       
carbon-nitrogen ligase act.. 0016884 1 7 53 16 6 6 27 2
spindle microtubule 0005876 2 13 54 19 38 38 42 2
organic acid metabolism 0006082 3 9 11 8 564 1619 3283 83
carboxylic acid metabolism 0019752 4 8 12 7 564 1619 3283 83
intramolecular isomerase act.. 0016863 5 10 10 12 195 412 453 4
deoxynucleoside kinase act.. 0019136 6 18 60 51 70 70 117 2
GMP synthase activity 0003921 7 27 317 78 6 6 6 1
intramolecular isomerase act.. 0016860 9 12 9 14 195 453 905 9
biotin metabolism 0006768 10 21 62 58 76 76 132 2
nucleus 0005634 71 16 28 10 1100 2353 3797 574
mitotic cell cycle 0000278 121 1 3 1 346 1419 3031 93
M phase 0000279 107 2 1 2 251 848 1862 41
nuclear division 0000280 124 3 2 3 251 867 1862 40
M phase of mitotic cell cycle 0000087 130 4 4 4 238 848 1862 36
mitosis 0007067 152 5 5 5 235 848 1862 35
cell cycle 0007049 142 6 6 6 731 1689 3599 172
cell proliferation 0008283 112 11 7 9 891 1947 3645 264
regulation of cell cycle 0000074 153 29 8 15 731 1689 3604 105