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Supplementary Information

Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia

Section V: Outcome Analysis

Table S15. Probe sets most strongly associated with time to progression or relapse in the training set

  U133 probe set Gene description Symbol Location GenBank reference UniGene reference P valuea cFDRb
1 60471_at§* Homo sapiens transcribed sequence with strong similarity to protein ref:NP_079108.1 hypothetical protein FLJ22439 --- --- AA625133 Hs.512736 0.0001 0.4864
2 202283_at§ serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1 SERPINF1 Chr:17p13.1 NM_002615 Hs.173594 0.0001 0.4872
3 200682_s_at ubiquitin-conjugating enzyme E2L 3 UBE2L3 Chr:22q11.21 BG531983 Hs.108104 0.0004 0.4885
4 217208_s_at discs, large homolog 1 (Drosophila) DLG1 Chr:3q29 AL121981 Hs.389893 0.0004 0.4886
5 203063_at§* protein phosphatase 1F (PP2C domain containing) PPM1F Chr:22q11.22 NM_014634 Hs.278441 0.0004 0.4886
6 40420_at serine/threonine kinase 10 STK10 Chr:5q35.1 AB015718 Hs.16134 0.0004 0.4888
7 210720_s_at amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein APBA2BP Chr:20q11.22 AB039947 Hs.324104 0.0004 0.4889
8 209011_at triple functional domain (PTPRF interacting) TRIO Chr:5p15.1-p14 BF223718 Hs.367689 0.0005 0.4891
9 218117_at ring-box 1 RBX1 Chr:22q13.2 NM_014248 Hs.373992 0.0005 0.4891
10 60528_at phospholipase A2, group IVB (cytosolic) PLA2G4B Chr:15q11.2-q21.3 N71116 Hs.198161 0.0005 0.4896
11 38269_at protein kinase D2 PRKD2 Chr:19q13.2 AL050147 Hs.205431 0.0005 0.4896
12 219457_s_at Ras and Rab interactor 3 RIN3 Chr:14q32.13 NM_024832 Hs.413374 0.0008 0.4911
13 209707_at phosphatidylinositol glycan, class K PIGK Chr:1p31.1 AF022913 Hs.293653 0.0008 0.4914
14 218184_at tubby like protein 4 TULP4 Chr:6q25-q26 NM_020245 Hs.102237 0.0009 0.4917
15 214682_at polycystic kidney disease 1 (autosomal dominant) PKD1 Chr:16p13.3 AK023376 Hs.75813 0.0009 0.4917
16 212656_at hepatocellularcarcinoma-associated antigen HCA557a DKFZP586D0919 Chr:12q13.2 AF110399 Hs.435643 0.0009 0.4919
17 212129_at non-imprinted in Prader-Willi/Angelman syndrome 2 NIPA2 Chr:15q11.2 AI589507 Hs.512761 0.0010 0.4921
18 202650_s_at KIAA0195 gene product KIAA0195 Chr:17q25.3 NM_014738 Hs.301132 0.0010 0.4923
19 209553_at KIAA0804 protein KIAA0804 Chr:3q28 BC001001 Hs.361493 0.0010 0.4924
20 203241_at UV radiation resistance associated gene UVRAG Chr:11q13.5 NM_003369 Hs.13137 0.0010 0.4925
21 217329_x_at --- --- --- AF042164 --- 0.0011 0.4927
22 201381_x_at Siah-interacting protein SIP Chr:1q24-q25 AF057356 Hs.27258 0.0012 0.4930
23 209039_x_at EH-domain containing 1 EHD1 Chr:11q13 AF001434 Hs.155119 0.0012 0.4933
24 37384_at protein phosphatase 1F (PP2C domain containing) PPM1F Chr:22q11.22 D86995 Hs.278441 0.0013 0.4935
25 202308_at sterol regulatory element binding transcription factor 1 SREBF1 Chr:17p11.2 NM_004176 Hs.426528 0.0013 0.4935
26 212096_s_at mitochondrial tumor suppressor gene 1 MTSG1 Chr:8p22 AL096842 Hs.7946 0.0013 0.4935
27 221945_at KIAA1940 protein KIAA1940 Chr:2p13.2 AA906578 Hs.23158 0.0013 0.4936
28 200773_x_at prothymosin, alpha (gene sequence 28) PTMA Chr:2q35-q36 NM_002823 Hs.459927 0.0013 0.4937
29 219933_at glutaredoxin 2 GLRX2 Chr:1q31.2-q31.3 NM_016066 Hs.458283 0.0014 0.4940
30 219416_at scavenger receptor class A, member 3 SCARA3 Chr:8p21 NM_016240 Hs.128856 0.0014 0.4941
31 218336_at prefoldin 2 PFDN2 Chr:1q23.1 NM_012394 Hs.298229 0.0014 0.4942
32 211113_s_at ATP-binding cassette, sub-family G (WHITE), member 1 ABCG1 Chr:21q22.3 U34919 Hs.369055 0.0014 0.4943
33 219033_at hypothetical protein FLJ21308 FLJ21308 Chr:5q11.2 NM_024615 Hs.310185 0.0015 0.4943
34 216033_s_at FYN oncogene related to SRC, FGR, YES FYN Chr:6q21 S74774 Hs.390567 0.0015 0.4944
35 202530_at mitogen-activated protein kinase 14 MAPK14 Chr:6p21.3-p21.2 NM_001315 Hs.79107 0.0017 0.4954
36 44146_at glucocorticoid modulatory element binding protein 2 GMEB2 Chr:20q13.33 AA045183 Hs.28906 0.0017 0.4955
37 214061_at unknown MGC21654 product MGC21654 Chr:8q24.13 AI017564 Hs.95631 0.0017 0.4955
38 211096_at --- --- --- BC003111 --- 0.0018 0.4959
39 203662_s_at tropomodulin 1 TMOD1 Chr:9q22.3 NM_003275 Hs.374849 0.0019 0.4960
40 45653_at polymerase delta-interacting protein 1 PDIP1 Chr:16p11.2 AW026481 Hs.106817 0.0019 0.4961
41 203047_at serine/threonine kinase 10 STK10 Chr:5q35.1 NM_005990 Hs.16134 0.0019 0.4962
42 217586_x_at Homo sapiens transcribed sequence with weak  similarity to protein ref:NP_062553.1 (H.sapiens)  hypothetical protein FLJ11267 [Homo sapiens] --- --- N35922 Hs.269852 0.0019 0.4962
43 218890_x_at mitochondrial ribosomal protein L35 MRPL35 Chr:2p11.2 NM_016622 Hs.433439 0.0020 0.4963
44 218226_s_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa NDUFB4 Chr:3q13.33 NM_004547 Hs.227750 0.0020 0.4964
45 218896_s_at ELG protein HSA277841 Chr:17p13.3 NM_018553 Hs.120963 0.0021 0.4967
46 213880_at G protein-coupled receptor 49 GPR49 Chr:12q22-q23 AL524520 Hs.166705 0.0022 0.4970
47 219539_at gem (nuclear organelle) associated protein 6 GEMIN6 Chr:2p22.3 NM_024775 Hs.143818 0.0022 0.4972
48 201840_at neural precursor cell expressed, developmentally down-regulated 8 NEDD8 Chr:14q11.2 NM_006156 Hs.75512 0.0023 0.4975
49 218461_at protein x 0004 MGC14560 Chr:12q24.13 NM_016301 Hs.284164 0.0024 0.4976
50 212477_at centaurin, beta 2 CENTB2 Chr:3q29 D26069 Hs.410715 0.0024 0.4976

a summary p represents a combined p value for the significance of association of expression with outcome in each treatment protocol as compared with the gamma distribution of three similarly transformed independent variables.
b conditional false discovery rate (cFDR) estimated using the LOESS histogram.
§ Probe sets with p-values less than or equal a = 0.001 in all 68 leave-one-out GMS assessments (jack-knife procedure).
* Significant in a multivariable Cox regression analysis including all probes selected by the jackknife procedure.