This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 18 focal events and 10 molecular subtypes across 123 patients, 94 significant findings detected with P value < 0.05 and Q value < 0.25.
-
amp_1q41 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
amp_12p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
amp_xq23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_2q37.1 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
-
del_3p22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6p25.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
del_9p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_10q26.3 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
del_19p13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
del_22q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
-
del_22q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 1q41 | 28 (23%) | 95 |
0.00028 (0.0012) |
1e-05 (9.47e-05) |
0.00027 (0.0012) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
1e-05 (9.47e-05) |
del 6p25 2 | 26 (21%) | 97 |
6e-05 (0.00036) |
1e-05 (9.47e-05) |
2e-05 (0.000164) |
0.00022 (0.00107) |
0.00213 (0.0071) |
6e-05 (0.00036) |
0.00136 (0.0048) |
0.00651 (0.018) |
1e-05 (9.47e-05) |
0.00632 (0.0178) |
del 6q21 | 20 (16%) | 103 |
3e-05 (0.000225) |
1e-05 (9.47e-05) |
0.0003 (0.00126) |
4e-05 (0.000277) |
1e-05 (9.47e-05) |
2e-05 (0.000164) |
1e-05 (9.47e-05) |
0.0002 (0.001) |
1e-05 (9.47e-05) |
6e-05 (0.00036) |
amp 12p12 3 | 6 (5%) | 117 |
0.0249 (0.0547) |
0.00054 (0.00211) |
0.193 (0.272) |
0.0291 (0.0608) |
0.0001 (0.000545) |
0.00032 (0.00128) |
0.0611 (0.112) |
0.00261 (0.00831) |
0.00873 (0.0221) |
0.0159 (0.0381) |
amp xq23 | 7 (6%) | 116 |
0.00238 (0.00779) |
5e-05 (0.000333) |
0.369 (0.459) |
0.157 (0.237) |
0.00839 (0.0216) |
0.0139 (0.0342) |
0.00399 (0.0116) |
0.0452 (0.0875) |
0.00263 (0.00831) |
0.0264 (0.056) |
del 3p22 2 | 14 (11%) | 109 |
0.00104 (0.0039) |
1e-05 (9.47e-05) |
0.052 (0.0985) |
4e-05 (0.000277) |
0.0322 (0.0659) |
0.0154 (0.0376) |
0.0161 (0.0381) |
0.0646 (0.117) |
0.00028 (0.0012) |
0.0399 (0.079) |
del 9p21 3 | 11 (9%) | 112 |
0.00025 (0.00118) |
0.00017 (9e-04) |
0.198 (0.276) |
0.00129 (0.00464) |
8e-05 (0.000465) |
1e-05 (9.47e-05) |
0.634 (0.692) |
0.00031 (0.00127) |
0.114 (0.179) |
0.0352 (0.0709) |
amp 17q11 2 | 10 (8%) | 113 |
1e-05 (9.47e-05) |
0.00319 (0.00973) |
0.0564 (0.105) |
0.0483 (0.0924) |
0.00139 (0.00481) |
2e-05 (0.000164) |
0.713 (0.751) |
0.0008 (0.00306) |
0.0796 (0.133) |
0.113 (0.179) |
del 9p22 1 | 6 (5%) | 117 |
3e-05 (0.000225) |
0.00831 (0.0216) |
0.0653 (0.117) |
0.131 (0.199) |
0.00286 (0.00888) |
9e-05 (0.000506) |
1 (1.00) |
0.00174 (0.00591) |
0.522 (0.599) |
0.12 (0.184) |
del 19p13 11 | 5 (4%) | 118 |
0.00018 (0.000926) |
0.0114 (0.0286) |
0.187 (0.269) |
0.203 (0.279) |
0.00387 (0.0114) |
0.00028 (0.0012) |
0.744 (0.775) |
0.00483 (0.0138) |
0.392 (0.473) |
0.242 (0.32) |
del 22q12 1 | 19 (15%) | 104 |
1e-05 (9.47e-05) |
0.0265 (0.056) |
0.0074 (0.0199) |
0.0536 (0.101) |
0.0189 (0.0435) |
0.073 (0.126) |
0.732 (0.766) |
0.457 (0.54) |
0.0247 (0.0547) |
0.459 (0.54) |
del 22q13 32 | 15 (12%) | 108 |
1e-05 (9.47e-05) |
0.0246 (0.0547) |
0.0438 (0.0857) |
0.0806 (0.133) |
0.0743 (0.127) |
0.0258 (0.056) |
0.595 (0.677) |
0.3 (0.391) |
0.0195 (0.0445) |
0.9 (0.931) |
del 7q36 3 | 3 (2%) | 120 |
0.00679 (0.0185) |
0.00755 (0.02) |
0.375 (0.46) |
0.202 (0.279) |
0.00125 (0.00459) |
0.00373 (0.0112) |
0.662 (0.707) |
0.117 (0.182) |
0.0756 (0.128) |
0.619 (0.683) |
del 10q26 3 | 6 (5%) | 117 |
0.37 (0.459) |
0.113 (0.179) |
0.184 (0.269) |
0.0318 (0.0658) |
0.0696 (0.122) |
0.219 (0.294) |
0.16 (0.24) |
0.0654 (0.117) |
0.52 (0.599) |
0.0354 (0.0709) |
del 2q37 1 | 5 (4%) | 118 |
0.598 (0.677) |
0.425 (0.51) |
0.191 (0.271) |
0.111 (0.179) |
0.672 (0.711) |
0.309 (0.4) |
1 (1.00) |
0.0188 (0.0435) |
0.64 (0.694) |
0.213 (0.289) |
amp 10q11 21 | 3 (2%) | 120 |
0.168 (0.248) |
0.0866 (0.142) |
0.0677 (0.119) |
0.188 (0.269) |
0.663 (0.707) |
0.105 (0.17) |
0.0761 (0.128) |
0.62 (0.683) |
||
amp 21q22 2 | 3 (2%) | 120 |
0.167 (0.248) |
0.381 (0.463) |
0.373 (0.46) |
0.205 (0.28) |
0.495 (0.578) |
0.188 (0.269) |
0.661 (0.707) |
0.344 (0.438) |
0.615 (0.683) |
0.622 (0.683) |
amp xp11 22 | 3 (2%) | 120 |
0.256 (0.336) |
0.522 (0.599) |
0.356 (0.448) |
0.328 (0.422) |
0.23 (0.307) |
0.615 (0.683) |
0.345 (0.438) |
0.44 (0.525) |
P value = 0.00028 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
AMP PEAK 1(1Q41) MUTATED | 14 | 0 | 7 | 4 | 3 |
AMP PEAK 1(1Q41) WILD-TYPE | 22 | 27 | 12 | 27 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
AMP PEAK 1(1Q41) MUTATED | 4 | 0 | 14 | 9 | 0 | 0 | 0 | 1 |
AMP PEAK 1(1Q41) WILD-TYPE | 33 | 23 | 5 | 1 | 18 | 8 | 2 | 5 |
P value = 0.00027 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
AMP PEAK 1(1Q41) MUTATED | 14 | 1 | 4 |
AMP PEAK 1(1Q41) WILD-TYPE | 17 | 24 | 30 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
AMP PEAK 1(1Q41) MUTATED | 0 | 0 | 5 | 14 |
AMP PEAK 1(1Q41) WILD-TYPE | 16 | 23 | 26 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
AMP PEAK 1(1Q41) MUTATED | 18 | 0 | 0 | 10 |
AMP PEAK 1(1Q41) WILD-TYPE | 27 | 30 | 30 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
AMP PEAK 1(1Q41) MUTATED | 20 | 0 | 0 | 8 |
AMP PEAK 1(1Q41) WILD-TYPE | 27 | 42 | 20 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 61 | 5 | 1 |
AMP PEAK 1(1Q41) MUTATED | 24 | 0 | 4 | 0 |
AMP PEAK 1(1Q41) WILD-TYPE | 32 | 61 | 1 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
AMP PEAK 1(1Q41) MUTATED | 10 | 0 | 12 | 6 | 0 | 0 |
AMP PEAK 1(1Q41) WILD-TYPE | 17 | 18 | 16 | 1 | 16 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
AMP PEAK 1(1Q41) MUTATED | 1 | 0 | 26 | 1 |
AMP PEAK 1(1Q41) WILD-TYPE | 27 | 51 | 17 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
AMP PEAK 1(1Q41) MUTATED | 9 | 0 | 19 | 0 |
AMP PEAK 1(1Q41) WILD-TYPE | 18 | 33 | 16 | 28 |
P value = 0.0249 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 4 | 1 | 0 |
AMP PEAK 3(12P12.3) WILD-TYPE | 35 | 27 | 15 | 30 | 10 |
P value = 0.00054 (Fisher's exact test), Q value = 0.0021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
AMP PEAK 3(12P12.3) MUTATED | 0 | 0 | 1 | 4 | 0 | 0 | 0 | 1 |
AMP PEAK 3(12P12.3) WILD-TYPE | 37 | 23 | 18 | 6 | 18 | 8 | 2 | 5 |
P value = 0.0291 (Fisher's exact test), Q value = 0.061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 0 | 3 |
AMP PEAK 3(12P12.3) WILD-TYPE | 15 | 23 | 31 | 17 |
P value = 1e-04 (Fisher's exact test), Q value = 0.00055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 0 | 5 |
AMP PEAK 3(12P12.3) WILD-TYPE | 44 | 30 | 30 | 9 |
P value = 0.00032 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 1 | 4 |
AMP PEAK 3(12P12.3) WILD-TYPE | 46 | 42 | 19 | 6 |
P value = 0.00261 (Fisher's exact test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 2 | 3 | 0 | 0 |
AMP PEAK 3(12P12.3) WILD-TYPE | 26 | 18 | 26 | 4 | 16 | 27 |
P value = 0.00873 (Fisher's exact test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
AMP PEAK 3(12P12.3) MUTATED | 0 | 0 | 6 | 0 |
AMP PEAK 3(12P12.3) WILD-TYPE | 28 | 51 | 37 | 1 |
P value = 0.0159 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
AMP PEAK 3(12P12.3) MUTATED | 1 | 0 | 5 | 0 |
AMP PEAK 3(12P12.3) WILD-TYPE | 26 | 33 | 30 | 28 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
AMP PEAK 4(17Q11.2) MUTATED | 0 | 2 | 8 | 0 | 0 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 36 | 25 | 11 | 31 | 10 |
P value = 0.00319 (Fisher's exact test), Q value = 0.0097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
AMP PEAK 4(17Q11.2) MUTATED | 1 | 3 | 1 | 5 | 0 | 0 | 0 | 0 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 36 | 20 | 18 | 5 | 18 | 8 | 2 | 6 |
P value = 0.0483 (Fisher's exact test), Q value = 0.092
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
AMP PEAK 4(17Q11.2) MUTATED | 1 | 2 | 0 | 4 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 15 | 21 | 31 | 16 |
P value = 0.00139 (Fisher's exact test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
AMP PEAK 4(17Q11.2) MUTATED | 2 | 0 | 3 | 5 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 43 | 30 | 27 | 9 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
AMP PEAK 4(17Q11.2) MUTATED | 2 | 0 | 3 | 5 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 45 | 42 | 17 | 5 |
P value = 8e-04 (Fisher's exact test), Q value = 0.0031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
AMP PEAK 4(17Q11.2) MUTATED | 1 | 0 | 2 | 3 | 4 | 0 |
AMP PEAK 4(17Q11.2) WILD-TYPE | 26 | 18 | 26 | 4 | 12 | 27 |
P value = 0.00238 (Fisher's exact test), Q value = 0.0078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
AMP PEAK 7(XQ23) MUTATED | 7 | 0 | 0 | 0 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 29 | 27 | 19 | 31 | 10 |
P value = 5e-05 (Fisher's exact test), Q value = 0.00033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
AMP PEAK 7(XQ23) MUTATED | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 37 | 23 | 12 | 10 | 18 | 8 | 2 | 6 |
P value = 0.00839 (Fisher's exact test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
AMP PEAK 7(XQ23) MUTATED | 7 | 0 | 0 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 38 | 30 | 30 | 14 |
P value = 0.0139 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
AMP PEAK 7(XQ23) MUTATED | 7 | 0 | 0 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 40 | 42 | 20 | 10 |
P value = 0.00399 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 61 | 5 | 1 |
AMP PEAK 7(XQ23) MUTATED | 5 | 0 | 2 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 51 | 61 | 3 | 1 |
P value = 0.0452 (Fisher's exact test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
AMP PEAK 7(XQ23) MUTATED | 5 | 0 | 2 | 0 | 0 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 22 | 18 | 26 | 7 | 16 | 27 |
P value = 0.00263 (Fisher's exact test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
AMP PEAK 7(XQ23) MUTATED | 0 | 0 | 7 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 28 | 51 | 36 | 1 |
P value = 0.0264 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
AMP PEAK 7(XQ23) MUTATED | 4 | 0 | 3 | 0 |
AMP PEAK 7(XQ23) WILD-TYPE | 23 | 33 | 32 | 28 |
P value = 0.0188 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 1(2Q37.1) MUTATED | 0 | 3 | 1 | 1 | 0 | 0 |
DEL PEAK 1(2Q37.1) WILD-TYPE | 27 | 15 | 27 | 6 | 16 | 27 |
P value = 0.00104 (Fisher's exact test), Q value = 0.0039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 2(3P22.2) MUTATED | 7 | 0 | 5 | 0 | 2 |
DEL PEAK 2(3P22.2) WILD-TYPE | 29 | 27 | 14 | 31 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 2(3P22.2) MUTATED | 0 | 1 | 9 | 3 | 1 | 0 | 0 | 0 |
DEL PEAK 2(3P22.2) WILD-TYPE | 37 | 22 | 10 | 7 | 17 | 8 | 2 | 6 |
P value = 4e-05 (Fisher's exact test), Q value = 0.00028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 2(3P22.2) MUTATED | 3 | 0 | 0 | 8 |
DEL PEAK 2(3P22.2) WILD-TYPE | 13 | 23 | 31 | 12 |
P value = 0.0322 (Fisher's exact test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 2(3P22.2) MUTATED | 9 | 1 | 1 | 3 |
DEL PEAK 2(3P22.2) WILD-TYPE | 36 | 29 | 29 | 11 |
P value = 0.0154 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 2(3P22.2) MUTATED | 10 | 1 | 1 | 2 |
DEL PEAK 2(3P22.2) WILD-TYPE | 37 | 41 | 19 | 8 |
P value = 0.0161 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 61 | 5 | 1 |
DEL PEAK 2(3P22.2) MUTATED | 11 | 2 | 1 | 0 |
DEL PEAK 2(3P22.2) WILD-TYPE | 45 | 59 | 4 | 1 |
P value = 0.00028 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
DEL PEAK 2(3P22.2) MUTATED | 0 | 2 | 12 | 0 |
DEL PEAK 2(3P22.2) WILD-TYPE | 28 | 49 | 31 | 1 |
P value = 0.0399 (Fisher's exact test), Q value = 0.079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
DEL PEAK 2(3P22.2) MUTATED | 6 | 1 | 6 | 1 |
DEL PEAK 2(3P22.2) WILD-TYPE | 21 | 32 | 29 | 27 |
P value = 6e-05 (Fisher's exact test), Q value = 0.00036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 3(6P25.2) MUTATED | 14 | 0 | 8 | 3 | 1 |
DEL PEAK 3(6P25.2) WILD-TYPE | 22 | 27 | 11 | 28 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 3(6P25.2) MUTATED | 1 | 2 | 13 | 7 | 3 | 0 | 0 | 0 |
DEL PEAK 3(6P25.2) WILD-TYPE | 36 | 21 | 6 | 3 | 15 | 8 | 2 | 6 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 3(6P25.2) MUTATED | 15 | 5 | 1 |
DEL PEAK 3(6P25.2) WILD-TYPE | 16 | 20 | 33 |
P value = 0.00022 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 3(6P25.2) MUTATED | 3 | 4 | 2 | 12 |
DEL PEAK 3(6P25.2) WILD-TYPE | 13 | 19 | 29 | 8 |
P value = 0.00213 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 3(6P25.2) MUTATED | 14 | 1 | 4 | 6 |
DEL PEAK 3(6P25.2) WILD-TYPE | 31 | 29 | 26 | 8 |
P value = 6e-05 (Fisher's exact test), Q value = 0.00036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 3(6P25.2) MUTATED | 15 | 4 | 0 | 6 |
DEL PEAK 3(6P25.2) WILD-TYPE | 32 | 38 | 20 | 4 |
P value = 0.00136 (Fisher's exact test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 61 | 5 | 1 |
DEL PEAK 3(6P25.2) MUTATED | 19 | 5 | 2 | 0 |
DEL PEAK 3(6P25.2) WILD-TYPE | 37 | 56 | 3 | 1 |
P value = 0.00651 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 3(6P25.2) MUTATED | 10 | 3 | 8 | 3 | 0 | 2 |
DEL PEAK 3(6P25.2) WILD-TYPE | 17 | 15 | 20 | 4 | 16 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
DEL PEAK 3(6P25.2) MUTATED | 0 | 5 | 21 | 0 |
DEL PEAK 3(6P25.2) WILD-TYPE | 28 | 46 | 22 | 1 |
P value = 0.00632 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
DEL PEAK 3(6P25.2) MUTATED | 9 | 3 | 12 | 2 |
DEL PEAK 3(6P25.2) WILD-TYPE | 18 | 30 | 23 | 26 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 4(6Q21) MUTATED | 11 | 0 | 8 | 1 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 25 | 27 | 11 | 30 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 4(6Q21) MUTATED | 1 | 0 | 12 | 6 | 0 | 0 | 0 | 1 |
DEL PEAK 4(6Q21) WILD-TYPE | 36 | 23 | 7 | 4 | 18 | 8 | 2 | 5 |
P value = 3e-04 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 4(6Q21) MUTATED | 12 | 2 | 1 |
DEL PEAK 4(6Q21) WILD-TYPE | 19 | 23 | 33 |
P value = 4e-05 (Fisher's exact test), Q value = 0.00028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 4(6Q21) MUTATED | 2 | 1 | 1 | 11 |
DEL PEAK 4(6Q21) WILD-TYPE | 14 | 22 | 30 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 4(6Q21) MUTATED | 13 | 0 | 0 | 7 |
DEL PEAK 4(6Q21) WILD-TYPE | 32 | 30 | 30 | 7 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 4(6Q21) MUTATED | 14 | 0 | 1 | 5 |
DEL PEAK 4(6Q21) WILD-TYPE | 33 | 42 | 19 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 61 | 5 | 1 |
DEL PEAK 4(6Q21) MUTATED | 17 | 1 | 2 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 39 | 60 | 3 | 1 |
P value = 2e-04 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 4(6Q21) MUTATED | 9 | 0 | 7 | 3 | 1 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 18 | 18 | 21 | 4 | 15 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
DEL PEAK 4(6Q21) MUTATED | 0 | 0 | 20 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 28 | 51 | 23 | 1 |
P value = 6e-05 (Fisher's exact test), Q value = 0.00036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
DEL PEAK 4(6Q21) MUTATED | 8 | 1 | 11 | 0 |
DEL PEAK 4(6Q21) WILD-TYPE | 19 | 32 | 24 | 28 |
P value = 0.00679 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 3 | 0 | 0 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 36 | 27 | 16 | 31 | 10 |
P value = 0.00755 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 1 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 37 | 23 | 19 | 8 | 18 | 8 | 2 | 5 |
P value = 0.00125 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 0 | 3 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 45 | 30 | 30 | 11 |
P value = 0.00373 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 5(7Q36.3) MUTATED | 0 | 0 | 1 | 2 |
DEL PEAK 5(7Q36.3) WILD-TYPE | 47 | 42 | 19 | 8 |
P value = 3e-05 (Fisher's exact test), Q value = 0.00022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 6(9P22.1) MUTATED | 0 | 0 | 6 | 0 | 0 |
DEL PEAK 6(9P22.1) WILD-TYPE | 36 | 27 | 13 | 31 | 10 |
P value = 0.00831 (Fisher's exact test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 6(9P22.1) MUTATED | 0 | 3 | 0 | 3 | 0 | 0 | 0 | 0 |
DEL PEAK 6(9P22.1) WILD-TYPE | 37 | 20 | 19 | 7 | 18 | 8 | 2 | 6 |
P value = 0.00286 (Fisher's exact test), Q value = 0.0089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 6(9P22.1) MUTATED | 0 | 0 | 3 | 3 |
DEL PEAK 6(9P22.1) WILD-TYPE | 45 | 30 | 27 | 11 |
P value = 9e-05 (Fisher's exact test), Q value = 0.00051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 6(9P22.1) MUTATED | 0 | 0 | 3 | 3 |
DEL PEAK 6(9P22.1) WILD-TYPE | 47 | 42 | 17 | 7 |
P value = 0.00174 (Fisher's exact test), Q value = 0.0059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 6(9P22.1) MUTATED | 0 | 0 | 1 | 2 | 3 | 0 |
DEL PEAK 6(9P22.1) WILD-TYPE | 27 | 18 | 27 | 5 | 13 | 27 |
P value = 0.00025 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 7(9P21.3) MUTATED | 1 | 0 | 7 | 2 | 1 |
DEL PEAK 7(9P21.3) WILD-TYPE | 35 | 27 | 12 | 29 | 9 |
P value = 0.00017 (Fisher's exact test), Q value = 9e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 7(9P21.3) MUTATED | 0 | 3 | 1 | 6 | 1 | 0 | 0 | 0 |
DEL PEAK 7(9P21.3) WILD-TYPE | 37 | 20 | 18 | 4 | 17 | 8 | 2 | 6 |
P value = 0.00129 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 7(9P21.3) MUTATED | 0 | 3 | 0 | 6 |
DEL PEAK 7(9P21.3) WILD-TYPE | 16 | 20 | 31 | 14 |
P value = 8e-05 (Fisher's exact test), Q value = 0.00046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 7(9P21.3) MUTATED | 1 | 0 | 3 | 6 |
DEL PEAK 7(9P21.3) WILD-TYPE | 44 | 30 | 27 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 7(9P21.3) MUTATED | 1 | 0 | 3 | 6 |
DEL PEAK 7(9P21.3) WILD-TYPE | 46 | 42 | 17 | 4 |
P value = 0.00031 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 7(9P21.3) MUTATED | 0 | 0 | 3 | 4 | 3 | 1 |
DEL PEAK 7(9P21.3) WILD-TYPE | 27 | 18 | 25 | 3 | 13 | 26 |
P value = 0.0352 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
DEL PEAK 7(9P21.3) MUTATED | 0 | 3 | 7 | 1 |
DEL PEAK 7(9P21.3) WILD-TYPE | 27 | 30 | 28 | 27 |
P value = 0.0318 (Fisher's exact test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 16 | 23 | 31 | 20 |
DEL PEAK 8(10Q26.3) MUTATED | 0 | 4 | 0 | 1 |
DEL PEAK 8(10Q26.3) WILD-TYPE | 16 | 19 | 31 | 19 |
P value = 0.0354 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 33 | 35 | 28 |
DEL PEAK 8(10Q26.3) MUTATED | 2 | 4 | 0 | 0 |
DEL PEAK 8(10Q26.3) WILD-TYPE | 25 | 29 | 35 | 28 |
P value = 0.00018 (Fisher's exact test), Q value = 0.00093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 9(19P13.11) MUTATED | 0 | 0 | 5 | 0 | 0 |
DEL PEAK 9(19P13.11) WILD-TYPE | 36 | 27 | 14 | 31 | 10 |
P value = 0.0114 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 9(19P13.11) MUTATED | 0 | 2 | 0 | 3 | 0 | 0 | 0 | 0 |
DEL PEAK 9(19P13.11) WILD-TYPE | 37 | 21 | 19 | 7 | 18 | 8 | 2 | 6 |
P value = 0.00387 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 9(19P13.11) MUTATED | 0 | 0 | 2 | 3 |
DEL PEAK 9(19P13.11) WILD-TYPE | 45 | 30 | 28 | 11 |
P value = 0.00028 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 9(19P13.11) MUTATED | 0 | 0 | 2 | 3 |
DEL PEAK 9(19P13.11) WILD-TYPE | 47 | 42 | 18 | 7 |
P value = 0.00483 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 27 | 18 | 28 | 7 | 16 | 27 |
DEL PEAK 9(19P13.11) MUTATED | 0 | 0 | 1 | 2 | 2 | 0 |
DEL PEAK 9(19P13.11) WILD-TYPE | 27 | 18 | 27 | 5 | 14 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 10(22Q12.1) MUTATED | 4 | 5 | 10 | 0 | 0 |
DEL PEAK 10(22Q12.1) WILD-TYPE | 32 | 22 | 9 | 31 | 10 |
P value = 0.0265 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 10(22Q12.1) MUTATED | 1 | 5 | 2 | 3 | 5 | 2 | 1 | 0 |
DEL PEAK 10(22Q12.1) WILD-TYPE | 36 | 18 | 17 | 7 | 13 | 6 | 1 | 6 |
P value = 0.0074 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 10(22Q12.1) MUTATED | 5 | 8 | 1 |
DEL PEAK 10(22Q12.1) WILD-TYPE | 26 | 17 | 33 |
P value = 0.0189 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 30 | 30 | 14 |
DEL PEAK 10(22Q12.1) MUTATED | 2 | 5 | 8 | 4 |
DEL PEAK 10(22Q12.1) WILD-TYPE | 43 | 25 | 22 | 10 |
P value = 0.0247 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
DEL PEAK 10(22Q12.1) MUTATED | 0 | 10 | 9 | 0 |
DEL PEAK 10(22Q12.1) WILD-TYPE | 28 | 41 | 34 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 36 | 27 | 19 | 31 | 10 |
DEL PEAK 11(22Q13.32) MUTATED | 2 | 2 | 11 | 0 | 0 |
DEL PEAK 11(22Q13.32) WILD-TYPE | 34 | 25 | 8 | 31 | 10 |
P value = 0.0246 (Fisher's exact test), Q value = 0.055
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 37 | 23 | 19 | 10 | 18 | 8 | 2 | 6 |
DEL PEAK 11(22Q13.32) MUTATED | 1 | 3 | 2 | 4 | 2 | 2 | 1 | 0 |
DEL PEAK 11(22Q13.32) WILD-TYPE | 36 | 20 | 17 | 6 | 16 | 6 | 1 | 6 |
P value = 0.0438 (Fisher's exact test), Q value = 0.086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 25 | 34 |
DEL PEAK 11(22Q13.32) MUTATED | 4 | 6 | 1 |
DEL PEAK 11(22Q13.32) WILD-TYPE | 27 | 19 | 33 |
P value = 0.0258 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 42 | 20 | 10 |
DEL PEAK 11(22Q13.32) MUTATED | 3 | 4 | 4 | 4 |
DEL PEAK 11(22Q13.32) WILD-TYPE | 44 | 38 | 16 | 6 |
P value = 0.0195 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 51 | 43 | 1 |
DEL PEAK 11(22Q13.32) MUTATED | 0 | 5 | 10 | 0 |
DEL PEAK 11(22Q13.32) WILD-TYPE | 28 | 46 | 33 | 1 |
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22516313/transformed.cor.cli.txt
-
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.transferedmergedcluster.txt
-
Number of patients = 123
-
Number of significantly focal cnvs = 18
-
Number of molecular subtypes = 10
-
Exclude genes that fewer than K tumors have alterations, K = 3
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
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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.