Table 1 |
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|
Comparison of RCMAT with the procedure of Kong et al. |
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|
Gene Set |
No. of Genes in Set |
RCMAT p-value |
Kong et al. p-value |
|
|
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|
c25_U133_probes |
64 |
0.0003 |
0.0039 |
|
MAP00600_Sphingoglycolipid_metabolism |
18 |
0.0018 |
0.0036 |
|
MAP00300_Lysine_biosynthesis |
5 |
0.002 |
0.0089 |
|
MAP00561_Glycerolipid_metabolism |
84 |
0.0028 |
0.7803 |
|
c29_U133_probes |
202 |
0.0033 |
0.0672 |
|
c33_U133_probes |
362 |
0.0034 |
0.1201 |
|
c23_U133_probes |
109 |
0.0035 |
0.1581 |
|
MAP00360_Phenylalanine_metabolism |
23 |
0.0036 |
0.0723 |
|
MAP00531_Glycosaminoglycan_degradation |
18 |
0.0043 |
0.0005 |
|
MAP00511_N_Glycan_degradation |
9 |
0.0072 |
0.0066 |
|
GLUCO_HG-U133A_probes |
46 |
0.0084 |
0.4585 |
|
GLYCOL_HG-U133A_probes |
31 |
0.0088 |
0.5699 |
|
MAP00910_Nitrogen_metabolism |
31 |
0.0094 |
0.0385 |
|
MAP00430_Taurine_and_hypotaurine_metabolism |
12 |
0.01 |
0.0888 |
|
mitochondr_HG-U133A_probes |
615 |
0.0107 |
0.05 |
|
MAP00650_Butanoate_metabolism |
38 |
0.0109 |
0.3458 |
|
human_mitoDB_6_2002_HG-U133A_probes |
594 |
0.0113 |
0.0381 |
|
c28_U133_probes |
288 |
0.0123 |
0.1947 |
|
MAP00252_Alanine_and_aspartate_metabolism |
35 |
0.0131 |
0.0472 |
|
c20_U133_probes |
270 |
0.0139 |
0.1125 |
|
MAP00190_Oxidative_phosphorylation |
75 |
0.0141 |
0.2173 |
|
c22_U133_probes |
194 |
0.0152 |
0.016 |
|
MAP00710_Carbon_fixation |
27 |
0.0152 |
0.0297 |
|
MAP00340_Histidine_metabolism |
32 |
0.0154 |
0.2045 |
|
MAP00330_Arginine_and_proline_metabolism |
63 |
0.0168 |
0.0062 |
|
c31_U133_probes |
346 |
0.0172 |
0.3197 |
|
MAP00380_Tryptophan_metabolism |
88 |
0.018 |
0.7238 |
|
MAP00380_Tryptophan_metabolism~ |
88 |
0.0195 |
0.7156 |
|
c7_U133_probes |
349 |
0.0207 |
0.1292 |
|
c15_U133_probes |
264 |
0.0232 |
0.4323 |
|
MAP00512_O_Glycans_biosynthesis |
15 |
0.0236 |
0.0322 |
|
MAP00970_Aminoacyl_tRNA_biosynthesis |
34 |
0.024 |
0.1054 |
|
c27_U133_probes |
266 |
0.0253 |
0.1722 |
|
MAP00251_Glutamate_metabolism |
35 |
0.0256 |
0.0259 |
|
c12_U133_probes |
251 |
0.0263 |
0.087 |
|
MAP00031_Inositol_metabolism |
7 |
0.0265 |
0.0677 |
|
MAP00410_beta_Alanine_metabolism |
27 |
0.0291 |
0.5854 |
|
c34_U133_probes |
452 |
0.0311 |
0.2366 |
|
c11_U133_probes |
192 |
0.0334 |
0.4341 |
|
c18_U133_probes |
248 |
0.0335 |
0.0167 |
|
MAP00590_Prostaglandin_and_leukotriene_metabolism |
34 |
0.0348 |
0.1956 |
|
c14_U133_probes |
302 |
0.0361 |
0.1327 |
|
c35_U133_probes |
470 |
0.0419 |
0.2794 |
|
OXPHOS_HG-U133A_probes |
114 |
0.0441 |
0.1705 |
|
ROS_HG-U133A_probes |
9 |
0.0446 |
0.1523 |
|
c3_U133_probes |
267 |
0.0455 |
0.5362 |
|
c30_U133_probes |
239 |
0.0462 |
0.1006 |
|
GO_0005739_HG-U133A_probes |
227 |
0.0467 |
0.3106 |
|
MAP00310_Lysine_degradation |
35 |
0.0477 |
0.4446 |
|
FA_HG-U133A_probes |
34 |
0.0485 |
0.1047 |
|
|
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|
For each of the gene sets from Mootha et al. [3] both the RCMAT and the method of Kong et al. were applied. Nominal (unadjusted) permutation p-values for each of the two procedures are given. The number of genes in the pathway is also provided. |
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|
Yates and Reimers BMC Bioinformatics 2009 10:300 doi:10.1186/1471-2105-10-300 |
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