Skip to main content

Table 1 Comparison of RCMAT with the procedure of Kong et al.

From: RCMAT: a regularized covariance matrix approach to testing gene sets

Gene Set No. of Genes in Set RCMAT
p-value
Kong et al.
p-value
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
  1. 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.