Rank Gender C1 Gender C2 P53 Diabetes
1 chrY testis genes from badpathway map00252 alanine
  (0.031, 0.031) xhx and netaffx (0.12, 0.14) and aspartate meta-
    (0.062, 0.062)   bolism(0.235, 0.206)
2 chrYp11 gnf female genes g2pathway mef2dpathway
  (0.031, 0.031) (0.125, 0.188) (0.14, 0.14) (0.235, 0.235)
3 chrYq11 xinact merged p53pathway achpathway
  (0.031, 0.031) (0.156, 0.125) (0.14, 0.18) (0.265, 0.324)
4 chrXp22 sig regulation of the drug resistance and ucalpainpathway
  (0.156, 0.156) actin cytoskeleton by metabolism(0.16, 0.24) (0.294, 0.324)
    rho gtpases(0.281, 0.25)    
5 chr12q15 st dictyostelium disco- mitochondriapathway map03020 rna poly-
  (0.281, 0.406) ideum camp chemotaxis (0.16, 0.14) merase(0.324, 0.294)
    pathway(0.281, 0.219)    
6 chr3q13 map00051 fructose and p53 signalling mprpathway
  (0.312, 0.281) mannose metabolism (0.16, 0.22) (0.324, 0.353)
    (0.312, 0.312)    
7 chrXp11 map00252 alanine and p53hypoxiapathway xinact merged
  (0.344, 0.281) aspartate metabolism (0.16, 0.2) (0.324, 0.206)
    (0.312, 0.344)    
8 chr2q14 map00910 nitrogen radiation sensitivity krebs-tca cycle
  (0.375, 0.406) metabolism(0.312, 0.25) (0.16, 0.18) (0.353, 0.294)
9 chrX cr dna met and mod p53 up map00710 carbon
  (0.375, 0.312) (0.344, 0.406) (0.16, 0.18) fixation(0.353, 0.324)
10 chr5p13 sig chemotaxis atmpathway s1p signaling
  (0.406, 0.375) (0.344, 0.219) (0.18, 0.18) (0.353, 0.412)
Rank Leukemia Lung Boston Lung Michigan  
1 chr3q25 vippathway cell adhesion molecule  
  (0, 0) (0.306, 0.355) activity(0.244, 0.256)  
2 chr8p21 map00330 arginine no1pathway  
  (0, 0) and proline meta- (0.244, 0.256)  
    bolism(0.339, 0.371)    
3 chr3q21 proteasome degrad- nfkb induced  
  (0, 0.021) ation(0.339, 0.355) (0.244, 0.267)  
4 chr7p15 p53 down hoxa9 down  
  (0, 0) (0.339, 0.258) (0.244, 0.244)  
5 chr3 hox list jp testis genes from  
  (0, 0.021) (0.339, 0.355) xhx and netaffx  
      (0.244, 0.244)  
6 chr11 downreg by hoxa9 alkpathway  
  (0, 0.042) (0.339, 0.355) (0.256, 0.267)  
7 chrY atmpathway at1rpathway  
  (0, 0) (0.355, 0.371) (0.256, 0.267)  
8 chr10q24 calcineurinpathway map00230 purine  
  (0.021, 0.021) (0.355, 0.355) metabolism(0.256, 0.279)  
9 chr8p11 cell growth and or map00860 porphyrin and  
  (0.021, 0.021) maintenance chlorophyll metabolism  
    (0.355, 0.387) (0.256, 0.256)  
10 chr3p25 g2pathway rac1pathway  
  (0.021, 0) (0.355, 0.306) (0.256, 0.267)  
Table 5: Results of real examples using pathwayRF. Top ten gene sets selected by the pathwayRF method for each data set. OOB and 5-fold cross-validation error rates are shown in parentheses.