Stomach Adenocarcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 75 peak regions and 6 molecular subtypes across 306 patients, 133 significant findings detected with Q value < 0.25.

- Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.

- Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- Amp Peak 4(3q26.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Amp Peak 6(5p13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 7(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 8(6q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 9(6q21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 10(7p22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 12(7q21.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 13(8p23.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 14(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 16(9q34.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 17(10q26.13) cnvs correlated to 'CN_CNMF'.

- Amp Peak 18(11p13) cnvs correlated to 'CN_CNMF'.

- Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 20(12p12.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF'.

- Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF'.

- Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Amp Peak 28(20q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 29(Xq26.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 4(2q32.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 9(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 10(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 12(6p25.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 13(6q26) cnvs correlated to 'CN_CNMF'.

- Del Peak 14(7q31.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 15(7q36.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 16(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 17(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 18(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 19(9q21.11) cnvs correlated to 'CN_CNMF'.

- Del Peak 20(10p14) cnvs correlated to 'CN_CNMF'.

- Del Peak 21(10q22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 22(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 23(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 24(11q23.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(12p13.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 26(13q14.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 27(14q21.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 28(14q32.33) cnvs correlated to 'CN_CNMF'.

- Del Peak 29(15q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 30(15q15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 31(16p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 32(16q23.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 33(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 34(17q24.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 35(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 36(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 37(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 46(Xq21.33) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
Del Peak 11(5q11 2) | 94 (31%) | 212 | 8.3e-27 (3.71e-24) | 2.93e-11 (1.19e-08) | 0.0452 (1.00) | 0.15 (1.00) | 2.27e-05 (0.00816) | 4.05e-06 (0.00149)
Del Peak 22(10q23 31) | 67 (22%) | 239 | 1.17e-18 (5.08e-16) | 1.36e-06 (0.000509) | 0.00684 (1.00) | 0.0899 (1.00) | 8.96e-05 (0.0309) | 4.69e-05 (0.0166)
Del Peak 37(19p13 3) | 91 (30%) | 215 | 2.75e-29 (1.24e-26) | 1.98e-12 (8.25e-10) | 0.347 (1.00) | 0.361 (1.00) | 0.000169 (0.0571) | 5.79e-09 (2.27e-06)
Amp Peak 3(1q42 3) | 95 (31%) | 211 | 6e-18 (2.59e-15) | 1.68e-06 (0.000623) | 0.755 (1.00) | 0.361 (1.00) | 9.69e-05 (0.0331) | 0.00587 (1.00)
Amp Peak 5(5p15 33) | 76 (25%) | 230 | 3.57e-19 (1.56e-16) | 1.8e-07 (6.84e-05) | 0.51 (1.00) | 0.476 (1.00) | 0.00824 (1.00) | 0.000785 (0.25)
Amp Peak 27(19q12) | 82 (27%) | 224 | 7.65e-18 (3.3e-15) | 2.2e-08 (8.59e-06) | 0.51 (1.00) | 0.0604 (1.00) | 0.0138 (1.00) | 1.13e-05 (0.00412)
Del Peak 9(4q22 1) | 120 (39%) | 186 | 1.51e-25 (6.75e-23) | 1.3e-07 (4.96e-05) | 0.223 (1.00) | 0.543 (1.00) | 0.00334 (0.993) | 0.000205 (0.0684)
Del Peak 10(4q34 3) | 111 (36%) | 195 | 9.9e-21 (4.37e-18) | 1.78e-06 (0.000659) | 0.0305 (1.00) | 0.165 (1.00) | 0.0138 (1.00) | 6.39e-05 (0.0223)
Del Peak 16(8p23 2) | 71 (23%) | 235 | 3.78e-18 (1.64e-15) | 2.17e-06 (0.000805) | 0.51 (1.00) | 0.899 (1.00) | 0.0474 (1.00) | 0.000177 (0.0595)
Del Peak 29(15q11 2) | 73 (24%) | 233 | 2.4e-16 (1.02e-13) | 2.86e-05 (0.0102) | 0.00934 (1.00) | 0.011 (1.00) | 0.01 (1.00) | 0.000107 (0.0362)
Del Peak 30(15q15 1) | 75 (25%) | 231 | 3.92e-15 (1.66e-12) | 9.19e-05 (0.0315) | 0.0452 (1.00) | 0.0899 (1.00) | 0.0354 (1.00) | 5.96e-05 (0.0209)
Del Peak 33(17p12) | 103 (34%) | 203 | 8.32e-32 (3.74e-29) | 9.36e-08 (3.59e-05) | 0.203 (1.00) | 0.509 (1.00) | 0.00142 (0.442) | 2.01e-05 (0.00723)
Del Peak 38(19q13 11) | 40 (13%) | 266 | 1.39e-10 (5.61e-08) | 0.000142 (0.048) | 0.0946 (1.00) | 0.23 (1.00) | 0.00354 (1.00) | 5.22e-05 (0.0184)
Del Peak 43(22q13 31) | 91 (30%) | 215 | 1.61e-19 (7.05e-17) | 1.05e-06 (0.000396) | 1 (1.00) | 1 (1.00) | 0.00277 (0.829) | 0.00019 (0.0637)
Amp Peak 2(1q21 3) | 101 (33%) | 205 | 3.9e-22 (1.73e-19) | 4.87e-11 (1.98e-08) | 0.215 (1.00) | 0.0203 (1.00) | 0.0008 (0.253) | 0.00164 (0.509)
Amp Peak 6(5p13 1) | 74 (24%) | 232 | 1.03e-18 (4.47e-16) | 9.23e-06 (0.00337) | 1 (1.00) | 0.561 (1.00) | 0.0316 (1.00) | 0.00525 (1.00)
Amp Peak 7(6p21 1) | 74 (24%) | 232 | 2.54e-17 (1.09e-14) | 4.45e-07 (0.000168) | 0.332 (1.00) | 0.678 (1.00) | 0.0368 (1.00) | 0.00115 (0.362)
Amp Peak 8(6q12) | 56 (18%) | 250 | 2.18e-10 (8.73e-08) | 1.77e-05 (0.00642) | 0.51 (1.00) | 0.899 (1.00) | 0.0669 (1.00) | 0.0179 (1.00)
Amp Peak 9(6q21) | 52 (17%) | 254 | 5.59e-09 (2.2e-06) | 0.000295 (0.0972) | 0.0883 (1.00) | 0.363 (1.00) | 0.241 (1.00) | 0.0216 (1.00)
Amp Peak 10(7p22 3) | 141 (46%) | 165 | 1.63e-22 (7.24e-20) | 5.91e-06 (0.00217) | 0.763 (1.00) | 0.428 (1.00) | 0.00811 (1.00) | 0.00208 (0.634)
Amp Peak 11(7p11 2) | 128 (42%) | 178 | 4.15e-20 (1.83e-17) | 0.000402 (0.131) | 0.547 (1.00) | 0.651 (1.00) | 0.00437 (1.00) | 0.0208 (1.00)
Amp Peak 14(8q24 21) | 186 (61%) | 120 | 5.82e-09 (2.28e-06) | 0.000497 (0.161) | 0.281 (1.00) | 0.464 (1.00) | 0.0838 (1.00) | 0.0202 (1.00)
Amp Peak 22(13q12 3) | 109 (36%) | 197 | 2.59e-12 (1.07e-09) | 0.000527 (0.17) | 0.223 (1.00) | 0.115 (1.00) | 0.408 (1.00) | 0.151 (1.00)
Amp Peak 23(13q22 1) | 118 (39%) | 188 | 2.32e-11 (9.46e-09) | 0.0013 (0.407) | 0.131 (1.00) | 0.652 (1.00) | 0.323 (1.00) | 0.000777 (0.248)
Amp Peak 24(15q26 1) | 65 (21%) | 241 | 5.77e-16 (2.45e-13) | 5.42e-05 (0.0191) | 1 (1.00) | 0.885 (1.00) | 0.0241 (1.00) | 0.0132 (1.00)
Amp Peak 28(20q13 2) | 191 (62%) | 115 | 1.98e-28 (8.85e-26) | 4.26e-07 (0.000161) | 0.755 (1.00) | 0.116 (1.00) | 0.0315 (1.00) | 0.0239 (1.00)
Del Peak 1(1p36 11) | 81 (26%) | 225 | 2.61e-14 (1.09e-11) | 0.000391 (0.128) | 0.358 (1.00) | 0.538 (1.00) | 0.0698 (1.00) | 0.0118 (1.00)
Del Peak 6(3p26 1) | 77 (25%) | 229 | 3.53e-12 (1.46e-09) | 0.000596 (0.192) | 0.185 (1.00) | 0.0899 (1.00) | 0.0623 (1.00) | 0.00525 (1.00)
Del Peak 7(3p14 2) | 97 (32%) | 209 | 4.66e-15 (1.96e-12) | 0.000101 (0.0343) | 0.488 (1.00) | 0.138 (1.00) | 0.205 (1.00) | 0.0138 (1.00)
Del Peak 12(6p25 3) | 66 (22%) | 240 | 7.12e-10 (2.83e-07) | 0.0029 (0.865) | 0.698 (1.00) | 0.424 (1.00) | 0.28 (1.00) | 0.000293 (0.0967)
Del Peak 15(7q36 3) | 55 (18%) | 251 | 3.8e-17 (1.62e-14) | 7.87e-06 (0.00288) | 0.698 (1.00) | 0.499 (1.00) | 0.179 (1.00) | 0.0017 (0.524)
Del Peak 17(9p23) | 110 (36%) | 196 | 1.59e-23 (7.07e-21) | 0.000285 (0.0943) | 0.124 (1.00) | 0.449 (1.00) | 0.0331 (1.00) | 0.0262 (1.00)
Del Peak 18(9p21 3) | 109 (36%) | 197 | 5.65e-23 (2.51e-20) | 1.19e-09 (4.69e-07) | 0.215 (1.00) | 0.839 (1.00) | 0.00662 (1.00) | 0.00243 (0.739)
Del Peak 21(10q22 3) | 46 (15%) | 260 | 4.02e-12 (1.65e-09) | 8.92e-05 (0.0309) | 0.132 (1.00) | 0.15 (1.00) | 0.0194 (1.00) | 0.00156 (0.485)
Del Peak 23(11p15 4) | 56 (18%) | 250 | 1.34e-10 (5.41e-08) | 0.000162 (0.0549) | 1 (1.00) | 1 (1.00) | 0.173 (1.00) | 0.00269 (0.806)
Del Peak 31(16p13 3) | 52 (17%) | 254 | 3.29e-12 (1.36e-09) | 0.000676 (0.217) | 1 (1.00) | 0.641 (1.00) | 0.0143 (1.00) | 0.181 (1.00)
Del Peak 35(18q21 2) | 124 (41%) | 182 | 8.77e-19 (3.83e-16) | 8.92e-05 (0.0309) | 0.763 (1.00) | 0.191 (1.00) | 0.112 (1.00) | 0.0142 (1.00)
Del Peak 36(18q23) | 116 (38%) | 190 | 1.21e-17 (5.2e-15) | 1.58e-05 (0.00573) | 1 (1.00) | 0.917 (1.00) | 0.0458 (1.00) | 0.00512 (1.00)
Del Peak 39(20p12 1) | 50 (16%) | 256 | 1.86e-10 (7.5e-08) | 7.73e-05 (0.0269) | 1 (1.00) | 0.84 (1.00) | 0.0244 (1.00) | 0.016 (1.00)
Del Peak 40(20p12 1) | 50 (16%) | 256 | 1.86e-10 (7.5e-08) | 7.73e-05 (0.0269) | 1 (1.00) | 0.84 (1.00) | 0.0244 (1.00) | 0.016 (1.00)
Del Peak 41(21q11 2) | 97 (32%) | 209 | 2.75e-15 (1.16e-12) | 0.00028 (0.0928) | 0.51 (1.00) | 0.899 (1.00) | 0.0115 (1.00) | 0.275 (1.00)
Del Peak 42(21q22 13) | 102 (33%) | 204 | 6.07e-16 (2.57e-13) | 0.000405 (0.131) | 0.215 (1.00) | 0.58 (1.00) | 0.0615 (1.00) | 0.143 (1.00)
Del Peak 44(Xp22 2) | 52 (17%) | 254 | 2.64e-14 (1.1e-11) | 0.000311 (0.102) | 0.698 (1.00) | 0.732 (1.00) | 0.131 (1.00) | 0.00839 (1.00)
Amp Peak 1(1p36 22) | 34 (11%) | 272 | 5.21e-09 (2.06e-06) | 0.00636 (1.00) | 0.412 (1.00) | 0.557 (1.00) | 0.0421 (1.00) | 0.181 (1.00)
Amp Peak 4(3q26 2) | 91 (30%) | 215 | 6.19e-08 (2.39e-05) | 0.00763 (1.00) | 0.116 (1.00) | 0.142 (1.00) | 0.0685 (1.00) | 0.378 (1.00)
Amp Peak 12(7q21 2) | 124 (41%) | 182 | 3.24e-18 (1.41e-15) | 0.00649 (1.00) | 0.547 (1.00) | 0.433 (1.00) | 0.0229 (1.00) | 0.0729 (1.00)
Amp Peak 13(8p23 1) | 114 (37%) | 192 | 6.18e-05 (0.0216) | 0.12 (1.00) | 0.364 (1.00) | 0.165 (1.00) | 0.558 (1.00) | 0.623 (1.00)
Amp Peak 16(9q34 3) | 67 (22%) | 239 | 1.35e-07 (5.15e-05) | 0.0609 (1.00) | 0.747 (1.00) | 1 (1.00) | 0.394 (1.00) | 0.313 (1.00)
Amp Peak 17(10q26 13) | 55 (18%) | 251 | 2.42e-05 (0.00867) | 0.0149 (1.00) | 1 (1.00) | 1 (1.00) | 0.447 (1.00) | 0.27 (1.00)
Amp Peak 18(11p13) | 48 (16%) | 258 | 0.000705 (0.226) | 0.265 (1.00) | 0.698 (1.00) | 0.293 (1.00) | 0.221 (1.00) | 0.07 (1.00)
Amp Peak 19(11q13 3) | 62 (20%) | 244 | 5.12e-08 (1.98e-05) | 0.0899 (1.00) | 1 (1.00) | 0.264 (1.00) | 0.0107 (1.00) | 0.05 (1.00)
Amp Peak 20(12p12 1) | 76 (25%) | 230 | 1.24e-06 (0.000464) | 0.00547 (1.00) | 0.412 (1.00) | 0.557 (1.00) | 0.16 (1.00) | 0.799 (1.00)
Amp Peak 21(12q15) | 69 (23%) | 237 | 3.03e-05 (0.0108) | 0.00484 (1.00) | 0.721 (1.00) | 1 (1.00) | 0.475 (1.00) | 0.804 (1.00)
Amp Peak 25(17q12) | 83 (27%) | 223 | 3.11e-17 (1.33e-14) | 0.00175 (0.538) | 0.736 (1.00) | 0.162 (1.00) | 0.0088 (1.00) | 0.00362 (1.00)
Amp Peak 26(18q11 2) | 80 (26%) | 226 | 9.1e-09 (3.56e-06) | 0.00203 (0.62) | 1 (1.00) | 0.616 (1.00) | 0.338 (1.00) | 0.164 (1.00)
Amp Peak 29(Xq26 2) | 60 (20%) | 246 | 2.69e-06 (0.000991) | 0.385 (1.00) | 0.281 (1.00) | 0.532 (1.00) | 0.0524 (1.00) | 0.929 (1.00)
Del Peak 2(1p13 2) | 55 (18%) | 251 | 2.42e-12 (1e-09) | 0.00674 (1.00) | 0.162 (1.00) | 0.707 (1.00) | 0.0524 (1.00) | 0.0308 (1.00)
Del Peak 4(2q32 1) | 34 (11%) | 272 | 0.000205 (0.0684) | 0.164 (1.00) | 0.664 (1.00) | 0.73 (1.00) | 0.279 (1.00) | 0.0614 (1.00)
Del Peak 5(2q37 2) | 40 (13%) | 266 | 4.33e-07 (0.000164) | 0.00694 (1.00) | 0.607 (1.00) | 0.643 (1.00) | 0.114 (1.00) | 0.00889 (1.00)
Del Peak 8(3q26 31) | 32 (10%) | 274 | 1.98e-05 (0.00715) | 0.00893 (1.00) | 0.345 (1.00) | 0.356 (1.00) | 0.0599 (1.00) | 0.00659 (1.00)
Del Peak 13(6q26) | 58 (19%) | 248 | 2.71e-07 (0.000103) | 0.0185 (1.00) | 0.457 (1.00) | 0.603 (1.00) | 0.223 (1.00) | 0.161 (1.00)
Del Peak 14(7q31 1) | 41 (13%) | 265 | 3.02e-08 (1.17e-05) | 0.00397 (1.00) | 0.412 (1.00) | 0.557 (1.00) | 0.0305 (1.00) | 0.0839 (1.00)
Del Peak 19(9q21 11) | 68 (22%) | 238 | 1.12e-14 (4.71e-12) | 0.00181 (0.554) | 0.698 (1.00) | 0.641 (1.00) | 0.0817 (1.00) | 0.00248 (0.749)
Del Peak 20(10p14) | 39 (13%) | 267 | 6.64e-08 (2.56e-05) | 0.00375 (1.00) | 0.721 (1.00) | 0.885 (1.00) | 0.0167 (1.00) | 0.0459 (1.00)
Del Peak 24(11q23 2) | 55 (18%) | 251 | 1.18e-06 (0.000444) | 0.000872 (0.276) | 1 (1.00) | 0.215 (1.00) | 0.0607 (1.00) | 0.221 (1.00)
Del Peak 25(12p13 31) | 46 (15%) | 260 | 2.28e-11 (9.35e-09) | 0.00244 (0.739) | 1 (1.00) | 1 (1.00) | 0.0802 (1.00) | 0.335 (1.00)
Del Peak 26(13q14 2) | 40 (13%) | 266 | 3.12e-05 (0.0111) | 0.0194 (1.00) | 0.412 (1.00) | 0.557 (1.00) | 0.404 (1.00) | 0.879 (1.00)
Del Peak 27(14q21 1) | 67 (22%) | 239 | 1.06e-09 (4.2e-07) | 0.0412 (1.00) | 0.132 (1.00) | 0.674 (1.00) | 0.0343 (1.00) | 0.0177 (1.00)
Del Peak 28(14q32 33) | 81 (26%) | 225 | 2.7e-10 (1.08e-07) | 0.037 (1.00) | 0.0883 (1.00) | 0.458 (1.00) | 0.251 (1.00) | 0.174 (1.00)
Del Peak 32(16q23 1) | 104 (34%) | 202 | 1.13e-10 (4.57e-08) | 0.0266 (1.00) | 0.543 (1.00) | 0.915 (1.00) | 0.665 (1.00) | 0.182 (1.00)
Del Peak 34(17q24 3) | 50 (16%) | 256 | 9.38e-12 (3.85e-09) | 0.0225 (1.00) | 0.0883 (1.00) | 0.0551 (1.00) | 0.0145 (1.00) | 0.00115 (0.362)
Del Peak 45(Xp21 1) | 45 (15%) | 261 | 1.54e-13 (6.43e-11) | 0.00459 (1.00) | 0.281 (1.00) | 0.283 (1.00) | 0.0208 (1.00) | 0.0762 (1.00)
Del Peak 46(Xq21 33) | 38 (12%) | 268 | 8.31e-08 (3.2e-05) | 0.00261 (0.784) | 0.457 (1.00) | 0.674 (1.00) | 0.0496 (1.00) | 0.0108 (1.00)
Amp Peak 15(9p24 1) | 45 (15%) | 261 | 0.0752 (1.00) | 0.107 (1.00) | 0.698 (1.00) | 0.159 (1.00) | 0.701 (1.00) | 0.353 (1.00)
Del Peak 3(1q44) | 21 (7%) | 285 | 0.0073 (1.00) | 0.0121 (1.00) | 0.412 (1.00) | 0.84 (1.00) | 0.209 (1.00) | 0.0617 (1.00)

'Amp Peak 1(1p36.22) mutation analysis' versus 'CN_CNMF'

P value = 5.21e-09 (Fisher's exact test), Q value = 2.1e-06

Table S1. Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 1(1P36.22) MUTATED | 2 | 28 | 4
AMP PEAK 1(1P36.22) WILD-TYPE | 151 | 90 | 31

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 3.9e-22 (Fisher's exact test), Q value = 1.7e-19

Table S2. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 2(1Q21.3) MUTATED | 12 | 72 | 17
AMP PEAK 2(1Q21.3) WILD-TYPE | 141 | 46 | 18

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.87e-11 (Fisher's exact test), Q value = 2e-08

Table S3. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 2(1Q21.3) MUTATED | 2 | 23 | 11 | 48
AMP PEAK 2(1Q21.3) WILD-TYPE | 35 | 56 | 53 | 30

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'CN_CNMF'

P value = 6e-18 (Fisher's exact test), Q value = 2.6e-15

Table S4. Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 3(1Q42.3) MUTATED | 13 | 62 | 20
AMP PEAK 3(1Q42.3) WILD-TYPE | 140 | 56 | 15

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00062

Table S5. Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 3(1Q42.3) MUTATED | 3 | 21 | 14 | 41
AMP PEAK 3(1Q42.3) WILD-TYPE | 34 | 58 | 50 | 37

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.69e-05 (Fisher's exact test), Q value = 0.033

Table S6. Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
AMP PEAK 3(1Q42.3) MUTATED | 19 | 10 | 43
AMP PEAK 3(1Q42.3) WILD-TYPE | 70 | 45 | 49

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 6.19e-08 (Fisher's exact test), Q value = 2.4e-05

Table S7. Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 4(3Q26.2) MUTATED | 23 | 52 | 16
AMP PEAK 4(3Q26.2) WILD-TYPE | 130 | 66 | 19

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 3.57e-19 (Fisher's exact test), Q value = 1.6e-16

Table S8. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 5(5P15.33) MUTATED | 8 | 62 | 6
AMP PEAK 5(5P15.33) WILD-TYPE | 145 | 56 | 29

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(5p15.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.8e-07 (Fisher's exact test), Q value = 6.8e-05

Table S9. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 5(5P15.33) MUTATED | 6 | 12 | 7 | 38
AMP PEAK 5(5P15.33) WILD-TYPE | 31 | 67 | 57 | 40

Figure S9. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 5(5p15.33) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000785 (Fisher's exact test), Q value = 0.25

Table S10. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
AMP PEAK 5(5P15.33) MUTATED | 26 | 20 | 13
AMP PEAK 5(5P15.33) WILD-TYPE | 33 | 84 | 60

Figure S10. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(5p13.1) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-18 (Fisher's exact test), Q value = 4.5e-16

Table S11. Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 6(5P13.1) MUTATED | 7 | 60 | 7
AMP PEAK 6(5P13.1) WILD-TYPE | 146 | 58 | 28

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5p13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.23e-06 (Fisher's exact test), Q value = 0.0034

Table S12. Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 6(5P13.1) MUTATED | 6 | 12 | 7 | 34
AMP PEAK 6(5P13.1) WILD-TYPE | 31 | 67 | 57 | 44

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 7(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 2.54e-17 (Fisher's exact test), Q value = 1.1e-14

Table S13. Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 7(6P21.1) MUTATED | 7 | 57 | 10
AMP PEAK 7(6P21.1) WILD-TYPE | 146 | 61 | 25

Figure S13. Get High-res Image Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(6p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.45e-07 (Fisher's exact test), Q value = 0.00017

Table S14. Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 7(6P21.1) MUTATED | 2 | 18 | 5 | 33
AMP PEAK 7(6P21.1) WILD-TYPE | 35 | 61 | 59 | 45

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 8(6q12) mutation analysis' versus 'CN_CNMF'

P value = 2.18e-10 (Fisher's exact test), Q value = 8.7e-08

Table S15. Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 8(6Q12) MUTATED | 7 | 41 | 8
AMP PEAK 8(6Q12) WILD-TYPE | 146 | 77 | 27

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(6q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0064

Table S16. Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 8(6Q12) MUTATED | 2 | 14 | 2 | 24
AMP PEAK 8(6Q12) WILD-TYPE | 35 | 65 | 62 | 54

Figure S16. Get High-res Image Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 9(6q21) mutation analysis' versus 'CN_CNMF'

P value = 5.59e-09 (Fisher's exact test), Q value = 2.2e-06

Table S17. Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 9(6Q21) MUTATED | 8 | 39 | 5
AMP PEAK 9(6Q21) WILD-TYPE | 145 | 79 | 30

Figure S17. Get High-res Image Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 9(6q21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000295 (Fisher's exact test), Q value = 0.097

Table S18. Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 9(6Q21) MUTATED | 1 | 12 | 4 | 22
AMP PEAK 9(6Q21) WILD-TYPE | 36 | 67 | 60 | 56

Figure S18. Get High-res Image Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 10(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.63e-22 (Fisher's exact test), Q value = 7.2e-20

Table S19. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 10(7P22.3) MUTATED | 29 | 82 | 30
AMP PEAK 10(7P22.3) WILD-TYPE | 124 | 36 | 5

Figure S19. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.91e-06 (Fisher's exact test), Q value = 0.0022

Table S20. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 10(7P22.3) MUTATED | 14 | 37 | 14 | 50
AMP PEAK 10(7P22.3) WILD-TYPE | 23 | 42 | 50 | 28

Figure S20. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.15e-20 (Fisher's exact test), Q value = 1.8e-17

Table S21. Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 11(7P11.2) MUTATED | 27 | 70 | 31
AMP PEAK 11(7P11.2) WILD-TYPE | 126 | 48 | 4

Figure S21. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000402 (Fisher's exact test), Q value = 0.13

Table S22. Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 11(7P11.2) MUTATED | 14 | 36 | 13 | 42
AMP PEAK 11(7P11.2) WILD-TYPE | 23 | 43 | 51 | 36

Figure S22. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 12(7q21.2) mutation analysis' versus 'CN_CNMF'

P value = 3.24e-18 (Fisher's exact test), Q value = 1.4e-15

Table S23. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 12(7Q21.2) MUTATED | 28 | 65 | 31
AMP PEAK 12(7Q21.2) WILD-TYPE | 125 | 53 | 4

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 13(8p23.1) mutation analysis' versus 'CN_CNMF'

P value = 6.18e-05 (Fisher's exact test), Q value = 0.022

Table S24. Gene #13: 'Amp Peak 13(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 13(8P23.1) MUTATED | 58 | 32 | 24
AMP PEAK 13(8P23.1) WILD-TYPE | 95 | 86 | 11

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 5.82e-09 (Fisher's exact test), Q value = 2.3e-06

Table S25. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 14(8Q24.21) MUTATED | 67 | 91 | 28
AMP PEAK 14(8Q24.21) WILD-TYPE | 86 | 27 | 7

Figure S25. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000497 (Fisher's exact test), Q value = 0.16

Table S26. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 14(8Q24.21) MUTATED | 15 | 47 | 29 | 58
AMP PEAK 14(8Q24.21) WILD-TYPE | 22 | 32 | 35 | 20

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 16(9q34.3) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-07 (Fisher's exact test), Q value = 5.2e-05

Table S27. Gene #16: 'Amp Peak 16(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 16(9Q34.3) MUTATED | 14 | 43 | 10
AMP PEAK 16(9Q34.3) WILD-TYPE | 139 | 75 | 25

Figure S27. Get High-res Image Gene #16: 'Amp Peak 16(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(10q26.13) mutation analysis' versus 'CN_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.0087

Table S28. Gene #17: 'Amp Peak 17(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 17(10Q26.13) MUTATED | 13 | 35 | 7
AMP PEAK 17(10Q26.13) WILD-TYPE | 140 | 83 | 28

Figure S28. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 18(11p13) mutation analysis' versus 'CN_CNMF'

P value = 0.000705 (Fisher's exact test), Q value = 0.23

Table S29. Gene #18: 'Amp Peak 18(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 18(11P13) MUTATED | 13 | 30 | 5
AMP PEAK 18(11P13) WILD-TYPE | 140 | 88 | 30

Figure S29. Get High-res Image Gene #18: 'Amp Peak 18(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 19(11q13.3) mutation analysis' versus 'CN_CNMF'

P value = 5.12e-08 (Fisher's exact test), Q value = 2e-05

Table S30. Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 19(11Q13.3) MUTATED | 12 | 42 | 8
AMP PEAK 19(11Q13.3) WILD-TYPE | 141 | 76 | 27

Figure S30. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00046

Table S31. Gene #20: 'Amp Peak 20(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 20(12P12.1) MUTATED | 19 | 46 | 11
AMP PEAK 20(12P12.1) WILD-TYPE | 134 | 72 | 24

Figure S31. Get High-res Image Gene #20: 'Amp Peak 20(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 21(12q15) mutation analysis' versus 'CN_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.011

Table S32. Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 21(12Q15) MUTATED | 19 | 42 | 8
AMP PEAK 21(12Q15) WILD-TYPE | 134 | 76 | 27

Figure S32. Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q12.3) mutation analysis' versus 'CN_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.1e-09

Table S33. Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 22(13Q12.3) MUTATED | 25 | 62 | 22
AMP PEAK 22(13Q12.3) WILD-TYPE | 128 | 56 | 13

Figure S33. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q12.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000527 (Fisher's exact test), Q value = 0.17

Table S34. Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 22(13Q12.3) MUTATED | 8 | 22 | 18 | 42
AMP PEAK 22(13Q12.3) WILD-TYPE | 29 | 57 | 46 | 36

Figure S34. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 2.32e-11 (Fisher's exact test), Q value = 9.5e-09

Table S35. Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 23(13Q22.1) MUTATED | 30 | 66 | 22
AMP PEAK 23(13Q22.1) WILD-TYPE | 123 | 52 | 13

Figure S35. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 23(13q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000777 (Fisher's exact test), Q value = 0.25

Table S36. Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
AMP PEAK 23(13Q22.1) MUTATED | 34 | 29 | 25
AMP PEAK 23(13Q22.1) WILD-TYPE | 25 | 75 | 48

Figure S36. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(15q26.1) mutation analysis' versus 'CN_CNMF'

P value = 5.77e-16 (Fisher's exact test), Q value = 2.5e-13

Table S37. Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 24(15Q26.1) MUTATED | 8 | 54 | 3
AMP PEAK 24(15Q26.1) WILD-TYPE | 145 | 64 | 32

Figure S37. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(15q26.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.019

Table S38. Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 24(15Q26.1) MUTATED | 1 | 16 | 9 | 29
AMP PEAK 24(15Q26.1) WILD-TYPE | 36 | 63 | 55 | 49

Figure S38. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 25(17q12) mutation analysis' versus 'CN_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 1.3e-14

Table S39. Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 25(17Q12) MUTATED | 12 | 64 | 7
AMP PEAK 25(17Q12) WILD-TYPE | 141 | 54 | 28

Figure S39. Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 26(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 9.1e-09 (Fisher's exact test), Q value = 3.6e-06

Table S40. Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 26(18Q11.2) MUTATED | 19 | 53 | 8
AMP PEAK 26(18Q11.2) WILD-TYPE | 134 | 65 | 27

Figure S40. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 27(19q12) mutation analysis' versus 'CN_CNMF'

P value = 7.65e-18 (Fisher's exact test), Q value = 3.3e-15

Table S41. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 27(19Q12) MUTATED | 11 | 64 | 7
AMP PEAK 27(19Q12) WILD-TYPE | 142 | 54 | 28

Figure S41. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 27(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.2e-08 (Fisher's exact test), Q value = 8.6e-06

Table S42. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 27(19Q12) MUTATED | 7 | 12 | 9 | 42
AMP PEAK 27(19Q12) WILD-TYPE | 30 | 67 | 55 | 36

Figure S42. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 27(19q12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0041

Table S43. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
AMP PEAK 27(19Q12) MUTATED | 29 | 21 | 10
AMP PEAK 27(19Q12) WILD-TYPE | 30 | 83 | 63

Figure S43. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-28 (Fisher's exact test), Q value = 8.8e-26

Table S44. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 28(20Q13.2) MUTATED | 50 | 108 | 33
AMP PEAK 28(20Q13.2) WILD-TYPE | 103 | 10 | 2

Figure S44. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.26e-07 (Fisher's exact test), Q value = 0.00016

Table S45. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
AMP PEAK 28(20Q13.2) MUTATED | 25 | 42 | 27 | 66
AMP PEAK 28(20Q13.2) WILD-TYPE | 12 | 37 | 37 | 12

Figure S45. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 29(Xq26.2) mutation analysis' versus 'CN_CNMF'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.00099

Table S46. Gene #29: 'Amp Peak 29(Xq26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
AMP PEAK 29(XQ26.2) MUTATED | 13 | 36 | 11
AMP PEAK 29(XQ26.2) WILD-TYPE | 140 | 82 | 24

Figure S46. Get High-res Image Gene #29: 'Amp Peak 29(Xq26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.11) mutation analysis' versus 'CN_CNMF'

P value = 2.61e-14 (Fisher's exact test), Q value = 1.1e-11

Table S47. Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 1(1P36.11) MUTATED | 12 | 58 | 11
DEL PEAK 1(1P36.11) WILD-TYPE | 141 | 60 | 24

Figure S47. Get High-res Image Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000391 (Fisher's exact test), Q value = 0.13

Table S48. Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 1(1P36.11) MUTATED | 2 | 20 | 11 | 30
DEL PEAK 1(1P36.11) WILD-TYPE | 35 | 59 | 53 | 48

Figure S48. Get High-res Image Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(1p13.2) mutation analysis' versus 'CN_CNMF'

P value = 2.42e-12 (Fisher's exact test), Q value = 1e-09

Table S49. Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 2(1P13.2) MUTATED | 6 | 44 | 5
DEL PEAK 2(1P13.2) WILD-TYPE | 147 | 74 | 30

Figure S49. Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 4(2q32.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.068

Table S50. Gene #33: 'Del Peak 4(2q32.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 4(2Q32.1) MUTATED | 7 | 24 | 3
DEL PEAK 4(2Q32.1) WILD-TYPE | 146 | 94 | 32

Figure S50. Get High-res Image Gene #33: 'Del Peak 4(2q32.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(2q37.2) mutation analysis' versus 'CN_CNMF'

P value = 4.33e-07 (Fisher's exact test), Q value = 0.00016

Table S51. Gene #34: 'Del Peak 5(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 5(2Q37.2) MUTATED | 5 | 27 | 8
DEL PEAK 5(2Q37.2) WILD-TYPE | 148 | 91 | 27

Figure S51. Get High-res Image Gene #34: 'Del Peak 5(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(3p26.1) mutation analysis' versus 'CN_CNMF'

P value = 3.53e-12 (Fisher's exact test), Q value = 1.5e-09

Table S52. Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 6(3P26.1) MUTATED | 12 | 50 | 15
DEL PEAK 6(3P26.1) WILD-TYPE | 141 | 68 | 20

Figure S52. Get High-res Image Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(3p26.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000596 (Fisher's exact test), Q value = 0.19

Table S53. Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 6(3P26.1) MUTATED | 7 | 20 | 6 | 30
DEL PEAK 6(3P26.1) WILD-TYPE | 30 | 59 | 58 | 48

Figure S53. Get High-res Image Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 4.66e-15 (Fisher's exact test), Q value = 2e-12

Table S54. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 7(3P14.2) MUTATED | 17 | 65 | 15
DEL PEAK 7(3P14.2) WILD-TYPE | 136 | 53 | 20

Figure S54. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.034

Table S55. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 7(3P14.2) MUTATED | 13 | 26 | 8 | 37
DEL PEAK 7(3P14.2) WILD-TYPE | 24 | 53 | 56 | 41

Figure S55. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(3q26.31) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0072

Table S56. Gene #37: 'Del Peak 8(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 8(3Q26.31) MUTATED | 5 | 24 | 3
DEL PEAK 8(3Q26.31) WILD-TYPE | 148 | 94 | 32

Figure S56. Get High-res Image Gene #37: 'Del Peak 8(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.51e-25 (Fisher's exact test), Q value = 6.7e-23

Table S57. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 9(4Q22.1) MUTATED | 17 | 84 | 19
DEL PEAK 9(4Q22.1) WILD-TYPE | 136 | 34 | 16

Figure S57. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 5e-05

Table S58. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 9(4Q22.1) MUTATED | 5 | 29 | 16 | 49
DEL PEAK 9(4Q22.1) WILD-TYPE | 32 | 50 | 48 | 29

Figure S58. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000205 (Fisher's exact test), Q value = 0.068

Table S59. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 9(4Q22.1) MUTATED | 36 | 31 | 23
DEL PEAK 9(4Q22.1) WILD-TYPE | 23 | 73 | 50

Figure S59. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q34.3) mutation analysis' versus 'CN_CNMF'

P value = 9.9e-21 (Fisher's exact test), Q value = 4.4e-18

Table S60. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 10(4Q34.3) MUTATED | 18 | 78 | 15
DEL PEAK 10(4Q34.3) WILD-TYPE | 135 | 40 | 20

Figure S60. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(4q34.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00066

Table S61. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 10(4Q34.3) MUTATED | 3 | 25 | 20 | 44
DEL PEAK 10(4Q34.3) WILD-TYPE | 34 | 54 | 44 | 34

Figure S61. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 10(4q34.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.39e-05 (Fisher's exact test), Q value = 0.022

Table S62. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 10(4Q34.3) MUTATED | 35 | 28 | 20
DEL PEAK 10(4Q34.3) WILD-TYPE | 24 | 76 | 53

Figure S62. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 8.3e-27 (Fisher's exact test), Q value = 3.7e-24

Table S63. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 11(5Q11.2) MUTATED | 8 | 76 | 10
DEL PEAK 11(5Q11.2) WILD-TYPE | 145 | 42 | 25

Figure S63. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.93e-11 (Fisher's exact test), Q value = 1.2e-08

Table S64. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 11(5Q11.2) MUTATED | 2 | 24 | 8 | 46
DEL PEAK 11(5Q11.2) WILD-TYPE | 35 | 55 | 56 | 32

Figure S64. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0082

Table S65. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
DEL PEAK 11(5Q11.2) MUTATED | 24 | 5 | 40
DEL PEAK 11(5Q11.2) WILD-TYPE | 65 | 50 | 52

Figure S65. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0015

Table S66. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 11(5Q11.2) MUTATED | 32 | 26 | 11
DEL PEAK 11(5Q11.2) WILD-TYPE | 27 | 78 | 62

Figure S66. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 7.12e-10 (Fisher's exact test), Q value = 2.8e-07

Table S67. Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 12(6P25.3) MUTATED | 13 | 48 | 5
DEL PEAK 12(6P25.3) WILD-TYPE | 140 | 70 | 30

Figure S67. Get High-res Image Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6p25.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.097

Table S68. Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 12(6P25.3) MUTATED | 23 | 17 | 8
DEL PEAK 12(6P25.3) WILD-TYPE | 36 | 87 | 65

Figure S68. Get High-res Image Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(6q26) mutation analysis' versus 'CN_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 1e-04

Table S69. Gene #42: 'Del Peak 13(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 13(6Q26) MUTATED | 11 | 38 | 9
DEL PEAK 13(6Q26) WILD-TYPE | 142 | 80 | 26

Figure S69. Get High-res Image Gene #42: 'Del Peak 13(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(7q31.1) mutation analysis' versus 'CN_CNMF'

P value = 3.02e-08 (Fisher's exact test), Q value = 1.2e-05

Table S70. Gene #43: 'Del Peak 14(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 14(7Q31.1) MUTATED | 6 | 33 | 2
DEL PEAK 14(7Q31.1) WILD-TYPE | 147 | 85 | 33

Figure S70. Get High-res Image Gene #43: 'Del Peak 14(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 3.8e-17 (Fisher's exact test), Q value = 1.6e-14

Table S71. Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 15(7Q36.3) MUTATED | 4 | 49 | 2
DEL PEAK 15(7Q36.3) WILD-TYPE | 149 | 69 | 33

Figure S71. Get High-res Image Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(7q36.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0029

Table S72. Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 15(7Q36.3) MUTATED | 0 | 16 | 5 | 25
DEL PEAK 15(7Q36.3) WILD-TYPE | 37 | 63 | 59 | 53

Figure S72. Get High-res Image Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 3.78e-18 (Fisher's exact test), Q value = 1.6e-15

Table S73. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 16(8P23.2) MUTATED | 8 | 59 | 4
DEL PEAK 16(8P23.2) WILD-TYPE | 145 | 59 | 31

Figure S73. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 8e-04

Table S74. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 16(8P23.2) MUTATED | 1 | 16 | 9 | 33
DEL PEAK 16(8P23.2) WILD-TYPE | 36 | 63 | 55 | 45

Figure S74. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.06

Table S75. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 16(8P23.2) MUTATED | 26 | 18 | 11
DEL PEAK 16(8P23.2) WILD-TYPE | 33 | 86 | 62

Figure S75. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-23 (Fisher's exact test), Q value = 7.1e-21

Table S76. Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 17(9P23) MUTATED | 17 | 82 | 11
DEL PEAK 17(9P23) WILD-TYPE | 136 | 36 | 24

Figure S76. Get High-res Image Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000285 (Fisher's exact test), Q value = 0.094

Table S77. Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 17(9P23) MUTATED | 7 | 26 | 16 | 42
DEL PEAK 17(9P23) WILD-TYPE | 30 | 53 | 48 | 36

Figure S77. Get High-res Image Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 18(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 5.65e-23 (Fisher's exact test), Q value = 2.5e-20

Table S78. Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 18(9P21.3) MUTATED | 17 | 81 | 11
DEL PEAK 18(9P21.3) WILD-TYPE | 136 | 37 | 24

Figure S78. Get High-res Image Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.19e-09 (Fisher's exact test), Q value = 4.7e-07

Table S79. Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 18(9P21.3) MUTATED | 2 | 26 | 15 | 48
DEL PEAK 18(9P21.3) WILD-TYPE | 35 | 53 | 49 | 30

Figure S79. Get High-res Image Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 4.7e-12

Table S80. Gene #48: 'Del Peak 19(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 19(9Q21.11) MUTATED | 8 | 53 | 7
DEL PEAK 19(9Q21.11) WILD-TYPE | 145 | 65 | 28

Figure S80. Get High-res Image Gene #48: 'Del Peak 19(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(10p14) mutation analysis' versus 'CN_CNMF'

P value = 6.64e-08 (Fisher's exact test), Q value = 2.6e-05

Table S81. Gene #49: 'Del Peak 20(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 20(10P14) MUTATED | 5 | 31 | 3
DEL PEAK 20(10P14) WILD-TYPE | 148 | 87 | 32

Figure S81. Get High-res Image Gene #49: 'Del Peak 20(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(10q22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.02e-12 (Fisher's exact test), Q value = 1.7e-09

Table S82. Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 21(10Q22.3) MUTATED | 3 | 38 | 5
DEL PEAK 21(10Q22.3) WILD-TYPE | 150 | 80 | 30

Figure S82. Get High-res Image Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(10q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.92e-05 (Fisher's exact test), Q value = 0.031

Table S83. Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 21(10Q22.3) MUTATED | 2 | 11 | 2 | 22
DEL PEAK 21(10Q22.3) WILD-TYPE | 35 | 68 | 62 | 56

Figure S83. Get High-res Image Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.17e-18 (Fisher's exact test), Q value = 5.1e-16

Table S84. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 22(10Q23.31) MUTATED | 5 | 56 | 6
DEL PEAK 22(10Q23.31) WILD-TYPE | 148 | 62 | 29

Figure S84. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00051

Table S85. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 22(10Q23.31) MUTATED | 4 | 13 | 4 | 32
DEL PEAK 22(10Q23.31) WILD-TYPE | 33 | 66 | 60 | 46

Figure S85. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.031

Table S86. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
DEL PEAK 22(10Q23.31) MUTATED | 24 | 2 | 28
DEL PEAK 22(10Q23.31) WILD-TYPE | 65 | 53 | 64

Figure S86. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.017

Table S87. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 22(10Q23.31) MUTATED | 22 | 27 | 5
DEL PEAK 22(10Q23.31) WILD-TYPE | 37 | 77 | 68

Figure S87. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11p15.4) mutation analysis' versus 'CN_CNMF'

P value = 1.34e-10 (Fisher's exact test), Q value = 5.4e-08

Table S88. Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 23(11P15.4) MUTATED | 10 | 44 | 2
DEL PEAK 23(11P15.4) WILD-TYPE | 143 | 74 | 33

Figure S88. Get High-res Image Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(11p15.4) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.055

Table S89. Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 23(11P15.4) MUTATED | 2 | 10 | 5 | 25
DEL PEAK 23(11P15.4) WILD-TYPE | 35 | 69 | 59 | 53

Figure S89. Get High-res Image Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 24(11q23.2) mutation analysis' versus 'CN_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00044

Table S90. Gene #53: 'Del Peak 24(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 24(11Q23.2) MUTATED | 12 | 38 | 5
DEL PEAK 24(11Q23.2) WILD-TYPE | 141 | 80 | 30

Figure S90. Get High-res Image Gene #53: 'Del Peak 24(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(12p13.31) mutation analysis' versus 'CN_CNMF'

P value = 2.28e-11 (Fisher's exact test), Q value = 9.3e-09

Table S91. Gene #54: 'Del Peak 25(12p13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 25(12P13.31) MUTATED | 4 | 38 | 4
DEL PEAK 25(12P13.31) WILD-TYPE | 149 | 80 | 31

Figure S91. Get High-res Image Gene #54: 'Del Peak 25(12p13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.011

Table S92. Gene #55: 'Del Peak 26(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 26(13Q14.2) MUTATED | 8 | 28 | 4
DEL PEAK 26(13Q14.2) WILD-TYPE | 145 | 90 | 31

Figure S92. Get High-res Image Gene #55: 'Del Peak 26(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(14q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 4.2e-07

Table S93. Gene #56: 'Del Peak 27(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 27(14Q21.1) MUTATED | 12 | 47 | 8
DEL PEAK 27(14Q21.1) WILD-TYPE | 141 | 71 | 27

Figure S93. Get High-res Image Gene #56: 'Del Peak 27(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(14q32.33) mutation analysis' versus 'CN_CNMF'

P value = 2.7e-10 (Fisher's exact test), Q value = 1.1e-07

Table S94. Gene #57: 'Del Peak 28(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 28(14Q32.33) MUTATED | 16 | 53 | 12
DEL PEAK 28(14Q32.33) WILD-TYPE | 137 | 65 | 23

Figure S94. Get High-res Image Gene #57: 'Del Peak 28(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-16 (Fisher's exact test), Q value = 1e-13

Table S95. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 29(15Q11.2) MUTATED | 7 | 54 | 12
DEL PEAK 29(15Q11.2) WILD-TYPE | 146 | 64 | 23

Figure S95. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.86e-05 (Fisher's exact test), Q value = 0.01

Table S96. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 29(15Q11.2) MUTATED | 5 | 17 | 7 | 34
DEL PEAK 29(15Q11.2) WILD-TYPE | 32 | 62 | 57 | 44

Figure S96. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.036

Table S97. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 29(15Q11.2) MUTATED | 26 | 21 | 9
DEL PEAK 29(15Q11.2) WILD-TYPE | 33 | 83 | 64

Figure S97. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(15q15.1) mutation analysis' versus 'CN_CNMF'

P value = 3.92e-15 (Fisher's exact test), Q value = 1.7e-12

Table S98. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 30(15Q15.1) MUTATED | 9 | 55 | 11
DEL PEAK 30(15Q15.1) WILD-TYPE | 144 | 63 | 24

Figure S98. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(15q15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.032

Table S99. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 30(15Q15.1) MUTATED | 6 | 16 | 7 | 33
DEL PEAK 30(15Q15.1) WILD-TYPE | 31 | 63 | 57 | 45

Figure S99. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(15q15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.021

Table S100. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 30(15Q15.1) MUTATED | 26 | 23 | 8
DEL PEAK 30(15Q15.1) WILD-TYPE | 33 | 81 | 65

Figure S100. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(16p13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 1.4e-09

Table S101. Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 31(16P13.3) MUTATED | 6 | 43 | 3
DEL PEAK 31(16P13.3) WILD-TYPE | 147 | 75 | 32

Figure S101. Get High-res Image Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 31(16p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000676 (Fisher's exact test), Q value = 0.22

Table S102. Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 31(16P13.3) MUTATED | 1 | 13 | 6 | 23
DEL PEAK 31(16P13.3) WILD-TYPE | 36 | 66 | 58 | 55

Figure S102. Get High-res Image Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 32(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.13e-10 (Fisher's exact test), Q value = 4.6e-08

Table S103. Gene #61: 'Del Peak 32(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 32(16Q23.1) MUTATED | 25 | 64 | 15
DEL PEAK 32(16Q23.1) WILD-TYPE | 128 | 54 | 20

Figure S103. Get High-res Image Gene #61: 'Del Peak 32(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'CN_CNMF'

P value = 8.32e-32 (Fisher's exact test), Q value = 3.7e-29

Table S104. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 33(17P12) MUTATED | 7 | 82 | 14
DEL PEAK 33(17P12) WILD-TYPE | 146 | 36 | 21

Figure S104. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.36e-08 (Fisher's exact test), Q value = 3.6e-05

Table S105. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 33(17P12) MUTATED | 5 | 24 | 12 | 46
DEL PEAK 33(17P12) WILD-TYPE | 32 | 55 | 52 | 32

Figure S105. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0072

Table S106. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 33(17P12) MUTATED | 33 | 32 | 13
DEL PEAK 33(17P12) WILD-TYPE | 26 | 72 | 60

Figure S106. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(17q24.3) mutation analysis' versus 'CN_CNMF'

P value = 9.38e-12 (Fisher's exact test), Q value = 3.8e-09

Table S107. Gene #63: 'Del Peak 34(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 34(17Q24.3) MUTATED | 4 | 39 | 7
DEL PEAK 34(17Q24.3) WILD-TYPE | 149 | 79 | 28

Figure S107. Get High-res Image Gene #63: 'Del Peak 34(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 8.77e-19 (Fisher's exact test), Q value = 3.8e-16

Table S108. Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 35(18Q21.2) MUTATED | 26 | 83 | 15
DEL PEAK 35(18Q21.2) WILD-TYPE | 127 | 35 | 20

Figure S108. Get High-res Image Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.92e-05 (Fisher's exact test), Q value = 0.031

Table S109. Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 35(18Q21.2) MUTATED | 15 | 29 | 13 | 45
DEL PEAK 35(18Q21.2) WILD-TYPE | 22 | 50 | 51 | 33

Figure S109. Get High-res Image Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 36(18q23) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-17 (Fisher's exact test), Q value = 5.2e-15

Table S110. Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 36(18Q23) MUTATED | 24 | 79 | 13
DEL PEAK 36(18Q23) WILD-TYPE | 129 | 39 | 22

Figure S110. Get High-res Image Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 36(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0057

Table S111. Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 36(18Q23) MUTATED | 14 | 25 | 11 | 44
DEL PEAK 36(18Q23) WILD-TYPE | 23 | 54 | 53 | 34

Figure S111. Get High-res Image Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 2.75e-29 (Fisher's exact test), Q value = 1.2e-26

Table S112. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 37(19P13.3) MUTATED | 5 | 75 | 11
DEL PEAK 37(19P13.3) WILD-TYPE | 148 | 43 | 24

Figure S112. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.98e-12 (Fisher's exact test), Q value = 8.3e-10

Table S113. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 37(19P13.3) MUTATED | 3 | 20 | 5 | 46
DEL PEAK 37(19P13.3) WILD-TYPE | 34 | 59 | 59 | 32

Figure S113. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.057

Table S114. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 89 | 55 | 92
DEL PEAK 37(19P13.3) MUTATED | 22 | 7 | 40
DEL PEAK 37(19P13.3) WILD-TYPE | 67 | 48 | 52

Figure S114. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-09 (Fisher's exact test), Q value = 2.3e-06

Table S115. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 37(19P13.3) MUTATED | 36 | 23 | 10
DEL PEAK 37(19P13.3) WILD-TYPE | 23 | 81 | 63

Figure S115. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(19q13.11) mutation analysis' versus 'CN_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 5.6e-08

Table S116. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 38(19Q13.11) MUTATED | 2 | 31 | 7
DEL PEAK 38(19Q13.11) WILD-TYPE | 151 | 87 | 28

Figure S116. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 38(19q13.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.048

Table S117. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 38(19Q13.11) MUTATED | 0 | 13 | 2 | 17
DEL PEAK 38(19Q13.11) WILD-TYPE | 37 | 66 | 62 | 61

Figure S117. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 38(19q13.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.018

Table S118. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 38(19Q13.11) MUTATED | 18 | 7 | 5
DEL PEAK 38(19Q13.11) WILD-TYPE | 41 | 97 | 68

Figure S118. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 39(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-10 (Fisher's exact test), Q value = 7.5e-08

Table S119. Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 39(20P12.1) MUTATED | 10 | 40 | 0
DEL PEAK 39(20P12.1) WILD-TYPE | 143 | 78 | 35

Figure S119. Get High-res Image Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 39(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.027

Table S120. Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 39(20P12.1) MUTATED | 4 | 14 | 2 | 24
DEL PEAK 39(20P12.1) WILD-TYPE | 33 | 65 | 62 | 54

Figure S120. Get High-res Image Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 40(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-10 (Fisher's exact test), Q value = 7.5e-08

Table S121. Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 40(20P12.1) MUTATED | 10 | 40 | 0
DEL PEAK 40(20P12.1) WILD-TYPE | 143 | 78 | 35

Figure S121. Get High-res Image Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 40(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.027

Table S122. Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 40(20P12.1) MUTATED | 4 | 14 | 2 | 24
DEL PEAK 40(20P12.1) WILD-TYPE | 33 | 65 | 62 | 54

Figure S122. Get High-res Image Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 41(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.75e-15 (Fisher's exact test), Q value = 1.2e-12

Table S123. Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 41(21Q11.2) MUTATED | 17 | 66 | 14
DEL PEAK 41(21Q11.2) WILD-TYPE | 136 | 52 | 21

Figure S123. Get High-res Image Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 41(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.093

Table S124. Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 41(21Q11.2) MUTATED | 4 | 26 | 15 | 37
DEL PEAK 41(21Q11.2) WILD-TYPE | 33 | 53 | 49 | 41

Figure S124. Get High-res Image Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 42(21q22.13) mutation analysis' versus 'CN_CNMF'

P value = 6.07e-16 (Fisher's exact test), Q value = 2.6e-13

Table S125. Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 42(21Q22.13) MUTATED | 18 | 68 | 16
DEL PEAK 42(21Q22.13) WILD-TYPE | 135 | 50 | 19

Figure S125. Get High-res Image Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(21q22.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000405 (Fisher's exact test), Q value = 0.13

Table S126. Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 42(21Q22.13) MUTATED | 4 | 26 | 16 | 37
DEL PEAK 42(21Q22.13) WILD-TYPE | 33 | 53 | 48 | 41

Figure S126. Get High-res Image Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 1.61e-19 (Fisher's exact test), Q value = 7.1e-17

Table S127. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 43(22Q13.31) MUTATED | 12 | 69 | 10
DEL PEAK 43(22Q13.31) WILD-TYPE | 141 | 49 | 25

Figure S127. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 4e-04

Table S128. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 43(22Q13.31) MUTATED | 2 | 23 | 11 | 38
DEL PEAK 43(22Q13.31) WILD-TYPE | 35 | 56 | 53 | 40

Figure S128. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.064

Table S129. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 59 | 104 | 73
DEL PEAK 43(22Q13.31) MUTATED | 29 | 27 | 12
DEL PEAK 43(22Q13.31) WILD-TYPE | 30 | 77 | 61

Figure S129. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.64e-14 (Fisher's exact test), Q value = 1.1e-11

Table S130. Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 44(XP22.2) MUTATED | 7 | 45 | 0
DEL PEAK 44(XP22.2) WILD-TYPE | 146 | 73 | 35

Figure S130. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 44(Xp22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.1

Table S131. Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 79 | 64 | 78
DEL PEAK 44(XP22.2) MUTATED | 0 | 13 | 9 | 23
DEL PEAK 44(XP22.2) WILD-TYPE | 37 | 66 | 55 | 55

Figure S131. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 45(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-13 (Fisher's exact test), Q value = 6.4e-11

Table S132. Gene #74: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 45(XP21.1) MUTATED | 3 | 40 | 2
DEL PEAK 45(XP21.1) WILD-TYPE | 150 | 78 | 33

Figure S132. Get High-res Image Gene #74: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 46(Xq21.33) mutation analysis' versus 'CN_CNMF'

P value = 8.31e-08 (Fisher's exact test), Q value = 3.2e-05

Table S133. Gene #75: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 153 | 118 | 35
DEL PEAK 46(XQ21.33) MUTATED | 4 | 29 | 5
DEL PEAK 46(XQ21.33) WILD-TYPE | 149 | 89 | 30

Figure S133. Get High-res Image Gene #75: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Molecular subtype file = STAD-TP.transferedmergedcluster.txt

- Number of patients = 306

- Number of copy number variation regions = 75

- Number of molecular subtypes = 6

- Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
[3] GISTIC_version2
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