This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 12 clinical features across 377 patients, 45 significant findings detected with P value < 0.05 and Q value < 0.25.
-
3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'PATHOLOGY_T_STAGE' and 'RACE'.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
CNMF clustering analysis on RPPA data identified 5 subtypes that correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
-
Consensus hierarchical clustering analysis on RPPA data identified 5 subtypes that correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', and 'RACE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'RACE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'RACE'.
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6 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', and 'GENDER'.
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5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'YEARS_TO_BIRTH' and 'GENDER'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
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5 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', 'GENDER', and 'RACE'.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.206 (0.393) |
0.953 (0.956) |
0.563 (0.714) |
0.0429 (0.12) |
0.00485 (0.0224) |
0.00337 (0.0169) |
0.384 (0.584) |
0.0555 (0.142) |
0.101 (0.229) |
0.00965 (0.0399) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
0.618 (0.734) |
9.51e-09 (1.14e-06) |
0.00207 (0.0127) |
0.0495 (0.132) |
4.66e-06 (0.000187) |
1.46e-05 (0.000292) |
4.53e-06 (0.000187) |
6.58e-06 (0.000198) |
0.00393 (0.0188) |
7.4e-05 (0.000986) |
PATHOLOGIC STAGE | Fisher's exact test |
0.166 (0.337) |
0.737 (0.819) |
5e-05 (0.000857) |
0.00159 (0.0119) |
0.00718 (0.0319) |
0.00211 (0.0127) |
0.0855 (0.21) |
0.948 (0.956) |
0.0304 (0.0961) |
0.133 (0.289) |
PATHOLOGY T STAGE | Fisher's exact test |
0.0454 (0.124) |
0.956 (0.956) |
0.00267 (0.0146) |
0.00191 (0.0127) |
0.00051 (0.00556) |
0.00014 (0.00168) |
0.0361 (0.108) |
0.88 (0.91) |
0.224 (0.402) |
0.178 (0.345) |
PATHOLOGY N STAGE | Fisher's exact test |
0.468 (0.659) |
0.573 (0.716) |
0.266 (0.453) |
0.725 (0.813) |
0.413 (0.619) |
0.172 (0.341) |
0.944 (0.956) |
0.532 (0.695) |
0.431 (0.639) |
0.449 (0.649) |
PATHOLOGY M STAGE | Fisher's exact test |
0.83 (0.878) |
0.287 (0.473) |
0.286 (0.473) |
0.643 (0.757) |
0.495 (0.659) |
0.488 (0.659) |
0.308 (0.5) |
0.351 (0.555) |
0.224 (0.402) |
0.384 (0.584) |
GENDER | Fisher's exact test |
0.672 (0.775) |
0.0156 (0.0594) |
0.254 (0.449) |
0.0424 (0.12) |
1e-05 (0.00024) |
6e-05 (9e-04) |
0.00201 (0.0127) |
0.0287 (0.0931) |
0.0396 (0.116) |
0.021 (0.0743) |
RADIATION THERAPY | Fisher's exact test |
0.835 (0.878) |
0.565 (0.714) |
0.492 (0.659) |
0.856 (0.893) |
0.0728 (0.182) |
0.22 (0.402) |
0.594 (0.727) |
0.14 (0.299) |
0.669 (0.775) |
0.0991 (0.229) |
HISTOLOGICAL TYPE | Fisher's exact test |
0.101 (0.229) |
0.0184 (0.0671) |
0.492 (0.659) |
0.0921 (0.221) |
0.00319 (0.0166) |
0.00096 (0.00872) |
0.0557 (0.142) |
0.691 (0.79) |
0.0318 (0.0978) |
0.331 (0.53) |
RESIDUAL TUMOR | Fisher's exact test |
0.372 (0.579) |
0.547 (0.706) |
0.532 (0.695) |
0.608 (0.73) |
0.014 (0.0561) |
0.0242 (0.0829) |
0.485 (0.659) |
0.702 (0.795) |
0.153 (0.318) |
0.214 (0.401) |
RACE | Fisher's exact test |
0.0158 (0.0594) |
0.00109 (0.00872) |
0.00106 (0.00872) |
0.00265 (0.0146) |
0.00079 (0.0079) |
0.0264 (0.0881) |
0.131 (0.289) |
0.268 (0.453) |
0.462 (0.659) |
0.00933 (0.0399) |
ETHNICITY | Fisher's exact test |
0.26 (0.452) |
0.584 (0.722) |
0.152 (0.318) |
0.796 (0.853) |
0.767 (0.836) |
0.608 (0.73) |
0.173 (0.341) |
0.446 (0.649) |
0.756 (0.833) |
0.782 (0.845) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 93 | 151 | 126 |
P value = 0.206 (logrank test), Q value = 0.39
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
subtype1 | 90 | 26 | 0.3 - 108.8 (19.9) |
subtype2 | 150 | 59 | 0.0 - 120.8 (19.3) |
subtype3 | 124 | 44 | 0.4 - 114.3 (20.5) |
P value = 0.618 (Kruskal-Wallis (anova)), Q value = 0.73
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
subtype1 | 92 | 57.4 (15.3) |
subtype2 | 149 | 60.3 (11.8) |
subtype3 | 125 | 59.9 (13.0) |
P value = 0.166 (Fisher's exact test), Q value = 0.34
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
subtype1 | 47 | 16 | 1 | 18 | 1 | 3 | 0 | 1 | 1 |
subtype2 | 60 | 42 | 1 | 26 | 5 | 4 | 0 | 0 | 1 |
subtype3 | 66 | 29 | 1 | 18 | 3 | 0 | 2 | 0 | 0 |
P value = 0.0454 (Fisher's exact test), Q value = 0.12
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
subtype1 | 50 | 16 | 20 | 4 |
subtype2 | 63 | 49 | 32 | 7 |
subtype3 | 70 | 30 | 25 | 1 |
P value = 0.468 (Fisher's exact test), Q value = 0.66
nPatients | 0 | 1 |
---|---|---|
ALL | 254 | 3 |
subtype1 | 63 | 1 |
subtype2 | 99 | 2 |
subtype3 | 92 | 0 |
P value = 0.83 (Fisher's exact test), Q value = 0.88
nPatients | 0 | 1 |
---|---|---|
ALL | 266 | 4 |
subtype1 | 58 | 1 |
subtype2 | 112 | 1 |
subtype3 | 96 | 2 |
P value = 0.672 (Fisher's exact test), Q value = 0.77
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
subtype1 | 29 | 64 |
subtype2 | 52 | 99 |
subtype3 | 37 | 89 |
P value = 0.835 (Fisher's exact test), Q value = 0.88
nPatients | NO | YES |
---|---|---|
ALL | 338 | 9 |
subtype1 | 83 | 3 |
subtype2 | 139 | 3 |
subtype3 | 116 | 3 |
P value = 0.101 (Fisher's exact test), Q value = 0.23
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
subtype1 | 3 | 89 | 1 |
subtype2 | 0 | 148 | 3 |
subtype3 | 0 | 123 | 3 |
P value = 0.372 (Fisher's exact test), Q value = 0.58
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 324 | 17 | 1 | 21 |
subtype1 | 79 | 4 | 0 | 7 |
subtype2 | 131 | 7 | 0 | 11 |
subtype3 | 114 | 6 | 1 | 3 |
P value = 0.0158 (Fisher's exact test), Q value = 0.059
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
subtype1 | 1 | 27 | 6 | 58 |
subtype2 | 0 | 73 | 8 | 68 |
subtype3 | 1 | 58 | 3 | 57 |
P value = 0.26 (Fisher's exact test), Q value = 0.45
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 16 | 335 |
subtype1 | 2 | 85 |
subtype2 | 10 | 135 |
subtype3 | 4 | 115 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 93 | 163 | 121 |
P value = 0.953 (logrank test), Q value = 0.96
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 371 | 132 | 0.0 - 120.8 (19.8) |
subtype1 | 90 | 33 | 0.0 - 108.8 (20.8) |
subtype2 | 162 | 57 | 0.2 - 120.8 (20.2) |
subtype3 | 119 | 42 | 0.2 - 114.3 (18.3) |
P value = 9.51e-09 (Kruskal-Wallis (anova)), Q value = 1.1e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 373 | 59.3 (13.4) |
subtype1 | 91 | 57.9 (15.2) |
subtype2 | 162 | 63.8 (9.9) |
subtype3 | 120 | 54.2 (14.2) |
P value = 0.737 (Fisher's exact test), Q value = 0.82
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 175 | 87 | 3 | 65 | 9 | 9 | 2 | 1 | 2 |
subtype1 | 42 | 19 | 0 | 19 | 4 | 4 | 0 | 1 | 0 |
subtype2 | 79 | 38 | 2 | 26 | 3 | 3 | 0 | 0 | 1 |
subtype3 | 54 | 30 | 1 | 20 | 2 | 2 | 2 | 0 | 1 |
P value = 0.956 (Fisher's exact test), Q value = 0.96
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 185 | 95 | 81 | 13 |
subtype1 | 43 | 22 | 23 | 3 |
subtype2 | 84 | 41 | 31 | 6 |
subtype3 | 58 | 32 | 27 | 4 |
P value = 0.573 (Fisher's exact test), Q value = 0.72
nPatients | 0 | 1 |
---|---|---|
ALL | 257 | 4 |
subtype1 | 65 | 2 |
subtype2 | 107 | 1 |
subtype3 | 85 | 1 |
P value = 0.287 (Fisher's exact test), Q value = 0.47
nPatients | 0 | 1 |
---|---|---|
ALL | 272 | 4 |
subtype1 | 64 | 0 |
subtype2 | 117 | 1 |
subtype3 | 91 | 3 |
P value = 0.0156 (Fisher's exact test), Q value = 0.059
nPatients | FEMALE | MALE |
---|---|---|
ALL | 122 | 255 |
subtype1 | 34 | 59 |
subtype2 | 40 | 123 |
subtype3 | 48 | 73 |
P value = 0.565 (Fisher's exact test), Q value = 0.71
nPatients | NO | YES |
---|---|---|
ALL | 345 | 9 |
subtype1 | 85 | 1 |
subtype2 | 152 | 4 |
subtype3 | 108 | 4 |
P value = 0.0184 (Fisher's exact test), Q value = 0.067
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 367 | 7 |
subtype1 | 3 | 87 | 3 |
subtype2 | 0 | 162 | 1 |
subtype3 | 0 | 118 | 3 |
P value = 0.547 (Fisher's exact test), Q value = 0.71
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 330 | 17 | 1 | 22 |
subtype1 | 76 | 5 | 0 | 8 |
subtype2 | 145 | 8 | 0 | 7 |
subtype3 | 109 | 4 | 1 | 7 |
P value = 0.00109 (Fisher's exact test), Q value = 0.0087
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 161 | 17 | 187 |
subtype1 | 0 | 29 | 9 | 52 |
subtype2 | 1 | 66 | 7 | 85 |
subtype3 | 1 | 66 | 1 | 50 |
P value = 0.584 (Fisher's exact test), Q value = 0.72
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 340 |
subtype1 | 4 | 84 |
subtype2 | 6 | 146 |
subtype3 | 8 | 110 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 41 | 75 | 19 | 23 | 24 | 2 |
P value = 0.563 (logrank test), Q value = 0.71
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 180 | 93 | 0.2 - 114.3 (17.6) |
subtype1 | 41 | 24 | 0.2 - 113.0 (13.6) |
subtype2 | 75 | 35 | 0.3 - 108.8 (20.0) |
subtype3 | 19 | 12 | 0.3 - 114.3 (26.9) |
subtype4 | 22 | 9 | 0.5 - 66.3 (13.4) |
subtype5 | 23 | 13 | 0.3 - 58.5 (14.6) |
P value = 0.00207 (Kruskal-Wallis (anova)), Q value = 0.013
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 180 | 60.2 (14.8) |
subtype1 | 39 | 61.9 (11.8) |
subtype2 | 75 | 64.5 (12.8) |
subtype3 | 19 | 56.5 (17.0) |
subtype4 | 23 | 53.8 (15.7) |
subtype5 | 24 | 53.3 (18.1) |
P value = 5e-05 (Fisher's exact test), Q value = 0.00086
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVB |
---|---|---|---|---|---|---|---|---|
ALL | 70 | 38 | 3 | 44 | 6 | 6 | 2 | 1 |
subtype1 | 9 | 10 | 0 | 11 | 4 | 4 | 0 | 0 |
subtype2 | 43 | 10 | 2 | 13 | 0 | 0 | 1 | 0 |
subtype3 | 6 | 6 | 0 | 4 | 0 | 0 | 0 | 1 |
subtype4 | 9 | 3 | 0 | 9 | 0 | 0 | 1 | 0 |
subtype5 | 3 | 9 | 1 | 7 | 2 | 2 | 0 | 0 |
P value = 0.00267 (Fisher's exact test), Q value = 0.015
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 73 | 43 | 56 | 9 |
subtype1 | 10 | 12 | 15 | 4 |
subtype2 | 44 | 11 | 17 | 2 |
subtype3 | 7 | 6 | 5 | 1 |
subtype4 | 9 | 5 | 9 | 0 |
subtype5 | 3 | 9 | 10 | 2 |
P value = 0.266 (Fisher's exact test), Q value = 0.45
nPatients | 0 | 1 |
---|---|---|
ALL | 110 | 3 |
subtype1 | 25 | 2 |
subtype2 | 37 | 0 |
subtype3 | 17 | 0 |
subtype4 | 15 | 0 |
subtype5 | 16 | 1 |
P value = 0.286 (Fisher's exact test), Q value = 0.47
nPatients | 0 | 1 |
---|---|---|
ALL | 130 | 3 |
subtype1 | 35 | 0 |
subtype2 | 46 | 1 |
subtype3 | 16 | 1 |
subtype4 | 13 | 1 |
subtype5 | 20 | 0 |
P value = 0.254 (Fisher's exact test), Q value = 0.45
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 113 |
subtype1 | 16 | 25 |
subtype2 | 22 | 53 |
subtype3 | 9 | 10 |
subtype4 | 12 | 11 |
subtype5 | 10 | 14 |
P value = 0.492 (Fisher's exact test), Q value = 0.66
nPatients | NO | YES |
---|---|---|
ALL | 163 | 3 |
subtype1 | 38 | 1 |
subtype2 | 64 | 1 |
subtype3 | 16 | 1 |
subtype4 | 23 | 0 |
subtype5 | 22 | 0 |
P value = 0.492 (Fisher's exact test), Q value = 0.66
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 2 | 178 | 2 |
subtype1 | 1 | 38 | 2 |
subtype2 | 1 | 74 | 0 |
subtype3 | 0 | 19 | 0 |
subtype4 | 0 | 23 | 0 |
subtype5 | 0 | 24 | 0 |
P value = 0.532 (Fisher's exact test), Q value = 0.69
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 147 | 11 | 1 | 16 |
subtype1 | 30 | 5 | 0 | 3 |
subtype2 | 61 | 5 | 1 | 4 |
subtype3 | 17 | 0 | 0 | 2 |
subtype4 | 20 | 0 | 0 | 3 |
subtype5 | 19 | 1 | 0 | 4 |
P value = 0.00106 (Fisher's exact test), Q value = 0.0087
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 52 | 12 | 111 |
subtype1 | 14 | 0 | 24 |
subtype2 | 9 | 7 | 56 |
subtype3 | 9 | 1 | 9 |
subtype4 | 10 | 1 | 11 |
subtype5 | 10 | 3 | 11 |
P value = 0.152 (Fisher's exact test), Q value = 0.32
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 161 |
subtype1 | 2 | 34 |
subtype2 | 2 | 67 |
subtype3 | 0 | 19 |
subtype4 | 3 | 18 |
subtype5 | 0 | 23 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 41 | 47 | 38 | 19 | 39 |
P value = 0.0429 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 182 | 94 | 0.2 - 114.3 (17.8) |
subtype1 | 40 | 19 | 0.3 - 114.3 (19.1) |
subtype2 | 47 | 21 | 0.3 - 108.8 (19.8) |
subtype3 | 37 | 22 | 0.2 - 81.7 (12.3) |
subtype4 | 19 | 13 | 0.4 - 60.9 (13.6) |
subtype5 | 39 | 19 | 0.3 - 90.7 (21.7) |
P value = 0.0495 (Kruskal-Wallis (anova)), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 182 | 60.4 (14.9) |
subtype1 | 41 | 56.2 (18.3) |
subtype2 | 47 | 63.2 (12.6) |
subtype3 | 36 | 60.9 (10.3) |
subtype4 | 19 | 53.8 (17.7) |
subtype5 | 39 | 64.3 (13.8) |
P value = 0.00159 (Fisher's exact test), Q value = 0.012
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVB |
---|---|---|---|---|---|---|---|---|
ALL | 71 | 38 | 3 | 45 | 6 | 6 | 2 | 1 |
subtype1 | 11 | 10 | 1 | 10 | 2 | 4 | 1 | 1 |
subtype2 | 28 | 6 | 1 | 6 | 0 | 0 | 1 | 0 |
subtype3 | 7 | 12 | 0 | 11 | 3 | 1 | 0 | 0 |
subtype4 | 4 | 5 | 0 | 8 | 1 | 0 | 0 | 0 |
subtype5 | 21 | 5 | 1 | 10 | 0 | 1 | 0 | 0 |
P value = 0.00191 (Fisher's exact test), Q value = 0.013
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 74 | 43 | 57 | 9 |
subtype1 | 11 | 12 | 15 | 3 |
subtype2 | 29 | 7 | 9 | 1 |
subtype3 | 8 | 14 | 14 | 2 |
subtype4 | 4 | 5 | 8 | 2 |
subtype5 | 22 | 5 | 11 | 1 |
P value = 0.725 (Fisher's exact test), Q value = 0.81
nPatients | 0 | 1 |
---|---|---|
ALL | 112 | 3 |
subtype1 | 32 | 2 |
subtype2 | 20 | 0 |
subtype3 | 22 | 1 |
subtype4 | 12 | 0 |
subtype5 | 26 | 0 |
P value = 0.643 (Fisher's exact test), Q value = 0.76
nPatients | 0 | 1 |
---|---|---|
ALL | 132 | 3 |
subtype1 | 32 | 2 |
subtype2 | 28 | 1 |
subtype3 | 32 | 0 |
subtype4 | 14 | 0 |
subtype5 | 26 | 0 |
P value = 0.0424 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 70 | 114 |
subtype1 | 24 | 17 |
subtype2 | 13 | 34 |
subtype3 | 13 | 25 |
subtype4 | 7 | 12 |
subtype5 | 13 | 26 |
P value = 0.856 (Fisher's exact test), Q value = 0.89
nPatients | NO | YES |
---|---|---|
ALL | 165 | 3 |
subtype1 | 39 | 0 |
subtype2 | 40 | 1 |
subtype3 | 34 | 1 |
subtype4 | 18 | 0 |
subtype5 | 34 | 1 |
P value = 0.0921 (Fisher's exact test), Q value = 0.22
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 2 | 180 | 2 |
subtype1 | 0 | 39 | 2 |
subtype2 | 0 | 47 | 0 |
subtype3 | 0 | 38 | 0 |
subtype4 | 0 | 19 | 0 |
subtype5 | 2 | 37 | 0 |
P value = 0.608 (Fisher's exact test), Q value = 0.73
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 148 | 12 | 1 | 16 |
subtype1 | 34 | 2 | 0 | 4 |
subtype2 | 37 | 4 | 1 | 2 |
subtype3 | 27 | 4 | 0 | 6 |
subtype4 | 17 | 0 | 0 | 2 |
subtype5 | 33 | 2 | 0 | 2 |
P value = 0.00265 (Fisher's exact test), Q value = 0.015
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 52 | 12 | 113 |
subtype1 | 15 | 1 | 25 |
subtype2 | 4 | 4 | 36 |
subtype3 | 17 | 1 | 18 |
subtype4 | 8 | 2 | 9 |
subtype5 | 8 | 4 | 25 |
P value = 0.796 (Fisher's exact test), Q value = 0.85
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 8 | 162 |
subtype1 | 3 | 37 |
subtype2 | 1 | 42 |
subtype3 | 1 | 33 |
subtype4 | 1 | 17 |
subtype5 | 2 | 33 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 68 | 88 | 74 | 71 | 70 |
P value = 0.00485 (logrank test), Q value = 0.022
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 365 | 130 | 0.0 - 120.8 (19.6) |
subtype1 | 65 | 32 | 0.3 - 120.8 (13.6) |
subtype2 | 88 | 29 | 0.3 - 102.7 (22.9) |
subtype3 | 72 | 26 | 0.2 - 114.3 (19.4) |
subtype4 | 70 | 22 | 0.0 - 107.1 (20.9) |
subtype5 | 70 | 21 | 0.4 - 108.8 (19.0) |
P value = 4.66e-06 (Kruskal-Wallis (anova)), Q value = 0.00019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 367 | 59.3 (13.4) |
subtype1 | 66 | 60.7 (13.3) |
subtype2 | 87 | 62.7 (12.4) |
subtype3 | 73 | 52.5 (13.8) |
subtype4 | 71 | 58.8 (12.9) |
subtype5 | 70 | 61.2 (12.8) |
P value = 0.00718 (Fisher's exact test), Q value = 0.032
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 171 | 86 | 3 | 65 | 8 | 9 | 2 | 1 | 2 |
subtype1 | 17 | 25 | 0 | 14 | 3 | 3 | 0 | 0 | 1 |
subtype2 | 55 | 13 | 1 | 12 | 1 | 0 | 0 | 0 | 0 |
subtype3 | 33 | 17 | 1 | 14 | 1 | 2 | 1 | 0 | 1 |
subtype4 | 35 | 13 | 0 | 9 | 2 | 3 | 1 | 1 | 0 |
subtype5 | 31 | 18 | 1 | 16 | 1 | 1 | 0 | 0 | 0 |
P value = 0.00051 (Fisher's exact test), Q value = 0.0056
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 181 | 94 | 80 | 13 |
subtype1 | 17 | 29 | 17 | 5 |
subtype2 | 57 | 14 | 14 | 2 |
subtype3 | 37 | 18 | 18 | 1 |
subtype4 | 38 | 15 | 13 | 4 |
subtype5 | 32 | 18 | 18 | 1 |
P value = 0.413 (Fisher's exact test), Q value = 0.62
nPatients | 0 | 1 |
---|---|---|
ALL | 252 | 4 |
subtype1 | 40 | 1 |
subtype2 | 61 | 0 |
subtype3 | 59 | 2 |
subtype4 | 41 | 1 |
subtype5 | 51 | 0 |
P value = 0.495 (Fisher's exact test), Q value = 0.66
nPatients | 0 | 1 |
---|---|---|
ALL | 266 | 4 |
subtype1 | 46 | 1 |
subtype2 | 64 | 0 |
subtype3 | 61 | 2 |
subtype4 | 43 | 1 |
subtype5 | 52 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00024
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 250 |
subtype1 | 20 | 48 |
subtype2 | 23 | 65 |
subtype3 | 38 | 36 |
subtype4 | 30 | 41 |
subtype5 | 10 | 60 |
P value = 0.0728 (Fisher's exact test), Q value = 0.18
nPatients | NO | YES |
---|---|---|
ALL | 339 | 9 |
subtype1 | 64 | 1 |
subtype2 | 81 | 1 |
subtype3 | 69 | 0 |
subtype4 | 63 | 2 |
subtype5 | 62 | 5 |
P value = 0.00319 (Fisher's exact test), Q value = 0.017
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 361 | 7 |
subtype1 | 0 | 66 | 2 |
subtype2 | 0 | 88 | 0 |
subtype3 | 0 | 73 | 1 |
subtype4 | 3 | 64 | 4 |
subtype5 | 0 | 70 | 0 |
P value = 0.014 (Fisher's exact test), Q value = 0.056
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 324 | 17 | 1 | 22 |
subtype1 | 54 | 6 | 0 | 7 |
subtype2 | 78 | 3 | 0 | 6 |
subtype3 | 69 | 1 | 0 | 4 |
subtype4 | 56 | 6 | 1 | 5 |
subtype5 | 67 | 1 | 0 | 0 |
P value = 0.00079 (Fisher's exact test), Q value = 0.0079
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 184 |
subtype1 | 1 | 25 | 8 | 32 |
subtype2 | 0 | 32 | 3 | 48 |
subtype3 | 0 | 48 | 1 | 24 |
subtype4 | 0 | 24 | 2 | 43 |
subtype5 | 1 | 29 | 3 | 37 |
P value = 0.767 (Fisher's exact test), Q value = 0.84
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 334 |
subtype1 | 4 | 58 |
subtype2 | 6 | 76 |
subtype3 | 3 | 70 |
subtype4 | 3 | 64 |
subtype5 | 2 | 66 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 55 | 56 | 116 | 87 | 57 |
P value = 0.00337 (logrank test), Q value = 0.017
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 365 | 130 | 0.0 - 120.8 (19.6) |
subtype1 | 53 | 29 | 0.2 - 107.1 (13.1) |
subtype2 | 56 | 17 | 0.0 - 90.3 (19.2) |
subtype3 | 116 | 42 | 0.3 - 120.8 (21.2) |
subtype4 | 83 | 27 | 0.2 - 114.3 (19.6) |
subtype5 | 57 | 15 | 0.4 - 108.8 (18.7) |
P value = 1.46e-05 (Kruskal-Wallis (anova)), Q value = 0.00029
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 367 | 59.3 (13.4) |
subtype1 | 53 | 61.3 (11.3) |
subtype2 | 55 | 61.9 (9.6) |
subtype3 | 115 | 61.9 (11.7) |
subtype4 | 87 | 51.7 (16.0) |
subtype5 | 57 | 60.9 (13.6) |
P value = 0.00211 (Fisher's exact test), Q value = 0.013
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 171 | 86 | 3 | 65 | 8 | 9 | 2 | 1 | 2 |
subtype1 | 11 | 17 | 0 | 15 | 4 | 3 | 0 | 0 | 0 |
subtype2 | 33 | 10 | 0 | 3 | 1 | 2 | 0 | 0 | 0 |
subtype3 | 62 | 25 | 1 | 17 | 2 | 1 | 0 | 0 | 1 |
subtype4 | 41 | 19 | 1 | 17 | 0 | 2 | 2 | 1 | 1 |
subtype5 | 24 | 15 | 1 | 13 | 1 | 1 | 0 | 0 | 0 |
P value = 0.00014 (Fisher's exact test), Q value = 0.0017
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 181 | 94 | 80 | 13 |
subtype1 | 11 | 20 | 20 | 4 |
subtype2 | 37 | 11 | 5 | 2 |
subtype3 | 63 | 28 | 19 | 5 |
subtype4 | 45 | 20 | 21 | 1 |
subtype5 | 25 | 15 | 15 | 1 |
P value = 0.172 (Fisher's exact test), Q value = 0.34
nPatients | 0 | 1 |
---|---|---|
ALL | 252 | 4 |
subtype1 | 33 | 1 |
subtype2 | 31 | 0 |
subtype3 | 77 | 0 |
subtype4 | 67 | 3 |
subtype5 | 44 | 0 |
P value = 0.488 (Fisher's exact test), Q value = 0.66
nPatients | 0 | 1 |
---|---|---|
ALL | 266 | 4 |
subtype1 | 39 | 0 |
subtype2 | 32 | 0 |
subtype3 | 83 | 1 |
subtype4 | 68 | 3 |
subtype5 | 44 | 0 |
P value = 6e-05 (Fisher's exact test), Q value = 9e-04
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 250 |
subtype1 | 23 | 32 |
subtype2 | 13 | 43 |
subtype3 | 35 | 81 |
subtype4 | 42 | 45 |
subtype5 | 8 | 49 |
P value = 0.22 (Fisher's exact test), Q value = 0.4
nPatients | NO | YES |
---|---|---|
ALL | 339 | 9 |
subtype1 | 52 | 1 |
subtype2 | 52 | 0 |
subtype3 | 107 | 2 |
subtype4 | 77 | 2 |
subtype5 | 51 | 4 |
P value = 0.00096 (Fisher's exact test), Q value = 0.0087
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 361 | 7 |
subtype1 | 0 | 50 | 5 |
subtype2 | 0 | 56 | 0 |
subtype3 | 0 | 114 | 2 |
subtype4 | 3 | 84 | 0 |
subtype5 | 0 | 57 | 0 |
P value = 0.0242 (Fisher's exact test), Q value = 0.083
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 324 | 17 | 1 | 22 |
subtype1 | 43 | 7 | 0 | 4 |
subtype2 | 46 | 4 | 0 | 4 |
subtype3 | 102 | 4 | 0 | 8 |
subtype4 | 79 | 1 | 1 | 6 |
subtype5 | 54 | 1 | 0 | 0 |
P value = 0.0264 (Fisher's exact test), Q value = 0.088
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 184 |
subtype1 | 0 | 26 | 1 | 27 |
subtype2 | 0 | 14 | 4 | 35 |
subtype3 | 0 | 45 | 6 | 59 |
subtype4 | 1 | 50 | 2 | 34 |
subtype5 | 1 | 23 | 4 | 29 |
P value = 0.608 (Fisher's exact test), Q value = 0.73
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 334 |
subtype1 | 3 | 51 |
subtype2 | 4 | 51 |
subtype3 | 7 | 98 |
subtype4 | 3 | 80 |
subtype5 | 1 | 54 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 40 | 64 | 92 | 85 | 50 | 41 |
P value = 0.384 (logrank test), Q value = 0.58
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 366 | 128 | 0.0 - 120.8 (19.8) |
subtype1 | 38 | 17 | 0.2 - 120.8 (14.6) |
subtype2 | 64 | 23 | 0.3 - 113.0 (21.9) |
subtype3 | 92 | 26 | 0.0 - 114.3 (21.3) |
subtype4 | 84 | 27 | 0.3 - 108.8 (18.1) |
subtype5 | 49 | 19 | 0.4 - 83.2 (24.5) |
subtype6 | 39 | 16 | 0.2 - 89.7 (18.2) |
P value = 4.53e-06 (Kruskal-Wallis (anova)), Q value = 0.00019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 368 | 59.2 (13.4) |
subtype1 | 38 | 61.5 (11.3) |
subtype2 | 63 | 64.8 (10.6) |
subtype3 | 92 | 57.0 (13.1) |
subtype4 | 85 | 61.9 (11.9) |
subtype5 | 50 | 54.0 (16.1) |
subtype6 | 40 | 54.1 (14.5) |
P value = 0.0855 (Fisher's exact test), Q value = 0.21
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 172 | 86 | 3 | 64 | 9 | 9 | 2 | 1 | 2 |
subtype1 | 19 | 6 | 0 | 10 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 26 | 20 | 1 | 8 | 3 | 1 | 0 | 0 | 0 |
subtype3 | 51 | 17 | 0 | 9 | 0 | 2 | 1 | 1 | 1 |
subtype4 | 44 | 19 | 0 | 14 | 3 | 2 | 0 | 0 | 0 |
subtype5 | 18 | 14 | 2 | 11 | 0 | 2 | 1 | 0 | 0 |
subtype6 | 14 | 10 | 0 | 12 | 1 | 1 | 0 | 0 | 0 |
P value = 0.0361 (Fisher's exact test), Q value = 0.11
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 182 | 94 | 80 | 13 |
subtype1 | 19 | 7 | 12 | 2 |
subtype2 | 27 | 23 | 11 | 3 |
subtype3 | 57 | 17 | 12 | 4 |
subtype4 | 45 | 19 | 17 | 3 |
subtype5 | 20 | 15 | 14 | 1 |
subtype6 | 14 | 13 | 14 | 0 |
P value = 0.944 (Fisher's exact test), Q value = 0.96
nPatients | 0 | 1 |
---|---|---|
ALL | 254 | 4 |
subtype1 | 28 | 0 |
subtype2 | 40 | 0 |
subtype3 | 55 | 1 |
subtype4 | 62 | 1 |
subtype5 | 38 | 1 |
subtype6 | 31 | 1 |
P value = 0.308 (Fisher's exact test), Q value = 0.5
nPatients | 0 | 1 |
---|---|---|
ALL | 269 | 4 |
subtype1 | 24 | 1 |
subtype2 | 45 | 0 |
subtype3 | 60 | 2 |
subtype4 | 66 | 0 |
subtype5 | 40 | 1 |
subtype6 | 34 | 0 |
P value = 0.00201 (Fisher's exact test), Q value = 0.013
nPatients | FEMALE | MALE |
---|---|---|
ALL | 119 | 253 |
subtype1 | 14 | 26 |
subtype2 | 18 | 46 |
subtype3 | 29 | 63 |
subtype4 | 16 | 69 |
subtype5 | 19 | 31 |
subtype6 | 23 | 18 |
P value = 0.594 (Fisher's exact test), Q value = 0.73
nPatients | NO | YES |
---|---|---|
ALL | 340 | 9 |
subtype1 | 39 | 0 |
subtype2 | 61 | 1 |
subtype3 | 83 | 2 |
subtype4 | 75 | 4 |
subtype5 | 46 | 2 |
subtype6 | 36 | 0 |
P value = 0.0557 (Fisher's exact test), Q value = 0.14
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 362 | 7 |
subtype1 | 0 | 40 | 0 |
subtype2 | 0 | 63 | 1 |
subtype3 | 3 | 88 | 1 |
subtype4 | 0 | 85 | 0 |
subtype5 | 0 | 47 | 3 |
subtype6 | 0 | 39 | 2 |
P value = 0.485 (Fisher's exact test), Q value = 0.66
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 325 | 17 | 1 | 22 |
subtype1 | 32 | 2 | 0 | 3 |
subtype2 | 53 | 3 | 0 | 6 |
subtype3 | 78 | 5 | 1 | 7 |
subtype4 | 79 | 3 | 0 | 2 |
subtype5 | 45 | 1 | 0 | 4 |
subtype6 | 38 | 3 | 0 | 0 |
P value = 0.131 (Fisher's exact test), Q value = 0.29
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 161 | 17 | 182 |
subtype1 | 0 | 16 | 5 | 19 |
subtype2 | 0 | 20 | 4 | 36 |
subtype3 | 0 | 35 | 5 | 47 |
subtype4 | 1 | 42 | 2 | 40 |
subtype5 | 0 | 27 | 1 | 22 |
subtype6 | 1 | 21 | 0 | 18 |
P value = 0.173 (Fisher's exact test), Q value = 0.34
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 335 |
subtype1 | 2 | 36 |
subtype2 | 4 | 55 |
subtype3 | 3 | 82 |
subtype4 | 1 | 82 |
subtype5 | 5 | 44 |
subtype6 | 3 | 36 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 44 | 97 | 57 | 126 | 48 |
P value = 0.0555 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 366 | 128 | 0.0 - 120.8 (19.8) |
subtype1 | 42 | 18 | 0.0 - 120.8 (16.9) |
subtype2 | 97 | 34 | 0.3 - 102.7 (21.8) |
subtype3 | 55 | 26 | 0.3 - 113.0 (16.0) |
subtype4 | 124 | 40 | 0.2 - 114.3 (21.5) |
subtype5 | 48 | 10 | 0.3 - 108.8 (17.9) |
P value = 6.58e-06 (Kruskal-Wallis (anova)), Q value = 2e-04
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 368 | 59.2 (13.4) |
subtype1 | 43 | 61.6 (11.0) |
subtype2 | 95 | 62.8 (11.7) |
subtype3 | 57 | 59.0 (13.6) |
subtype4 | 125 | 54.1 (14.8) |
subtype5 | 48 | 63.6 (9.9) |
P value = 0.948 (Fisher's exact test), Q value = 0.96
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 172 | 86 | 3 | 64 | 9 | 9 | 2 | 1 | 2 |
subtype1 | 21 | 7 | 0 | 11 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 45 | 23 | 1 | 11 | 4 | 1 | 0 | 0 | 0 |
subtype3 | 26 | 14 | 0 | 12 | 1 | 1 | 0 | 0 | 0 |
subtype4 | 57 | 30 | 2 | 21 | 1 | 5 | 2 | 1 | 1 |
subtype5 | 23 | 12 | 0 | 9 | 1 | 1 | 0 | 0 | 0 |
P value = 0.88 (Fisher's exact test), Q value = 0.91
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 182 | 94 | 80 | 13 |
subtype1 | 21 | 8 | 13 | 2 |
subtype2 | 49 | 26 | 17 | 5 |
subtype3 | 28 | 15 | 14 | 0 |
subtype4 | 60 | 33 | 26 | 5 |
subtype5 | 24 | 12 | 10 | 1 |
P value = 0.532 (Fisher's exact test), Q value = 0.69
nPatients | 0 | 1 |
---|---|---|
ALL | 254 | 4 |
subtype1 | 31 | 0 |
subtype2 | 59 | 0 |
subtype3 | 39 | 1 |
subtype4 | 88 | 3 |
subtype5 | 37 | 0 |
P value = 0.351 (Fisher's exact test), Q value = 0.55
nPatients | 0 | 1 |
---|---|---|
ALL | 269 | 4 |
subtype1 | 28 | 1 |
subtype2 | 65 | 0 |
subtype3 | 43 | 0 |
subtype4 | 94 | 3 |
subtype5 | 39 | 0 |
P value = 0.0287 (Fisher's exact test), Q value = 0.093
nPatients | FEMALE | MALE |
---|---|---|
ALL | 119 | 253 |
subtype1 | 14 | 30 |
subtype2 | 29 | 68 |
subtype3 | 19 | 38 |
subtype4 | 50 | 76 |
subtype5 | 7 | 41 |
P value = 0.14 (Fisher's exact test), Q value = 0.3
nPatients | NO | YES |
---|---|---|
ALL | 340 | 9 |
subtype1 | 41 | 1 |
subtype2 | 93 | 0 |
subtype3 | 50 | 1 |
subtype4 | 113 | 4 |
subtype5 | 43 | 3 |
P value = 0.691 (Fisher's exact test), Q value = 0.79
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 362 | 7 |
subtype1 | 0 | 44 | 0 |
subtype2 | 0 | 95 | 2 |
subtype3 | 0 | 56 | 1 |
subtype4 | 3 | 119 | 4 |
subtype5 | 0 | 48 | 0 |
P value = 0.702 (Fisher's exact test), Q value = 0.79
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 325 | 17 | 1 | 22 |
subtype1 | 35 | 3 | 0 | 3 |
subtype2 | 83 | 5 | 0 | 6 |
subtype3 | 50 | 2 | 0 | 5 |
subtype4 | 111 | 6 | 1 | 8 |
subtype5 | 46 | 1 | 0 | 0 |
P value = 0.268 (Fisher's exact test), Q value = 0.45
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 161 | 17 | 182 |
subtype1 | 0 | 18 | 5 | 21 |
subtype2 | 0 | 34 | 5 | 52 |
subtype3 | 0 | 32 | 2 | 22 |
subtype4 | 1 | 56 | 4 | 62 |
subtype5 | 1 | 21 | 1 | 25 |
P value = 0.446 (Fisher's exact test), Q value = 0.65
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 335 |
subtype1 | 3 | 40 |
subtype2 | 4 | 86 |
subtype3 | 3 | 52 |
subtype4 | 8 | 112 |
subtype5 | 0 | 45 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 110 | 81 | 104 | 51 |
P value = 0.101 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 340 | 120 | 0.0 - 120.8 (19.8) |
subtype1 | 107 | 46 | 0.3 - 120.8 (17.6) |
subtype2 | 80 | 28 | 0.2 - 107.1 (21.4) |
subtype3 | 104 | 31 | 0.3 - 108.8 (21.2) |
subtype4 | 49 | 15 | 0.0 - 90.3 (17.1) |
P value = 0.00393 (Kruskal-Wallis (anova)), Q value = 0.019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 342 | 59.2 (13.1) |
subtype1 | 108 | 58.6 (14.0) |
subtype2 | 80 | 58.1 (12.4) |
subtype3 | 104 | 63.1 (9.8) |
subtype4 | 50 | 54.3 (16.2) |
P value = 0.0304 (Fisher's exact test), Q value = 0.096
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 157 | 83 | 3 | 59 | 7 | 8 | 2 | 1 | 2 |
subtype1 | 47 | 26 | 0 | 26 | 5 | 5 | 0 | 0 | 0 |
subtype2 | 38 | 17 | 0 | 10 | 0 | 3 | 1 | 1 | 1 |
subtype3 | 51 | 26 | 1 | 14 | 0 | 0 | 0 | 0 | 1 |
subtype4 | 21 | 14 | 2 | 9 | 2 | 0 | 1 | 0 | 0 |
P value = 0.224 (Fisher's exact test), Q value = 0.4
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 167 | 91 | 73 | 12 |
subtype1 | 48 | 27 | 30 | 5 |
subtype2 | 42 | 20 | 13 | 5 |
subtype3 | 55 | 29 | 16 | 2 |
subtype4 | 22 | 15 | 14 | 0 |
P value = 0.431 (Fisher's exact test), Q value = 0.64
nPatients | 0 | 1 |
---|---|---|
ALL | 238 | 4 |
subtype1 | 81 | 3 |
subtype2 | 48 | 1 |
subtype3 | 70 | 0 |
subtype4 | 39 | 0 |
P value = 0.224 (Fisher's exact test), Q value = 0.4
nPatients | 0 | 1 |
---|---|---|
ALL | 255 | 4 |
subtype1 | 88 | 0 |
subtype2 | 49 | 2 |
subtype3 | 75 | 1 |
subtype4 | 43 | 1 |
P value = 0.0396 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 115 | 231 |
subtype1 | 45 | 65 |
subtype2 | 27 | 54 |
subtype3 | 24 | 80 |
subtype4 | 19 | 32 |
P value = 0.669 (Fisher's exact test), Q value = 0.77
nPatients | NO | YES |
---|---|---|
ALL | 315 | 9 |
subtype1 | 101 | 3 |
subtype2 | 73 | 2 |
subtype3 | 94 | 4 |
subtype4 | 47 | 0 |
P value = 0.0318 (Fisher's exact test), Q value = 0.098
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 2 | 337 | 7 |
subtype1 | 0 | 108 | 2 |
subtype2 | 2 | 77 | 2 |
subtype3 | 0 | 104 | 0 |
subtype4 | 0 | 48 | 3 |
P value = 0.153 (Fisher's exact test), Q value = 0.32
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 303 | 17 | 1 | 19 |
subtype1 | 96 | 5 | 0 | 6 |
subtype2 | 65 | 8 | 1 | 5 |
subtype3 | 97 | 3 | 0 | 3 |
subtype4 | 45 | 1 | 0 | 5 |
P value = 0.462 (Fisher's exact test), Q value = 0.66
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 155 | 16 | 163 |
subtype1 | 1 | 56 | 3 | 48 |
subtype2 | 0 | 31 | 4 | 42 |
subtype3 | 1 | 40 | 7 | 52 |
subtype4 | 0 | 28 | 2 | 21 |
P value = 0.756 (Fisher's exact test), Q value = 0.83
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 16 | 312 |
subtype1 | 5 | 98 |
subtype2 | 5 | 72 |
subtype3 | 3 | 94 |
subtype4 | 3 | 48 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 73 | 84 | 101 | 34 | 54 |
P value = 0.00965 (logrank test), Q value = 0.04
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 340 | 120 | 0.0 - 120.8 (19.8) |
subtype1 | 69 | 34 | 0.3 - 107.1 (16.0) |
subtype2 | 84 | 30 | 0.3 - 113.0 (21.8) |
subtype3 | 100 | 32 | 0.2 - 114.3 (21.4) |
subtype4 | 33 | 14 | 0.0 - 120.8 (15.5) |
subtype5 | 54 | 10 | 0.3 - 108.8 (19.4) |
P value = 7.4e-05 (Kruskal-Wallis (anova)), Q value = 0.00099
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 342 | 59.2 (13.1) |
subtype1 | 72 | 54.8 (13.1) |
subtype2 | 82 | 63.2 (11.1) |
subtype3 | 100 | 56.4 (15.0) |
subtype4 | 34 | 62.6 (11.1) |
subtype5 | 54 | 62.4 (10.4) |
P value = 0.133 (Fisher's exact test), Q value = 0.29
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 157 | 83 | 3 | 59 | 7 | 8 | 2 | 1 | 2 |
subtype1 | 27 | 17 | 0 | 20 | 2 | 2 | 0 | 0 | 1 |
subtype2 | 39 | 20 | 1 | 11 | 4 | 1 | 0 | 0 | 0 |
subtype3 | 44 | 25 | 2 | 13 | 0 | 4 | 2 | 1 | 0 |
subtype4 | 19 | 4 | 0 | 8 | 1 | 1 | 0 | 0 | 1 |
subtype5 | 28 | 17 | 0 | 7 | 0 | 0 | 0 | 0 | 0 |
P value = 0.178 (Fisher's exact test), Q value = 0.35
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 167 | 91 | 73 | 12 |
subtype1 | 28 | 19 | 23 | 3 |
subtype2 | 42 | 23 | 15 | 4 |
subtype3 | 49 | 28 | 19 | 3 |
subtype4 | 19 | 4 | 9 | 2 |
subtype5 | 29 | 17 | 7 | 0 |
P value = 0.449 (Fisher's exact test), Q value = 0.65
nPatients | 0 | 1 |
---|---|---|
ALL | 238 | 4 |
subtype1 | 50 | 1 |
subtype2 | 51 | 0 |
subtype3 | 68 | 3 |
subtype4 | 27 | 0 |
subtype5 | 42 | 0 |
P value = 0.384 (Fisher's exact test), Q value = 0.58
nPatients | 0 | 1 |
---|---|---|
ALL | 255 | 4 |
subtype1 | 54 | 1 |
subtype2 | 59 | 0 |
subtype3 | 73 | 2 |
subtype4 | 23 | 1 |
subtype5 | 46 | 0 |
P value = 0.021 (Fisher's exact test), Q value = 0.074
nPatients | FEMALE | MALE |
---|---|---|
ALL | 115 | 231 |
subtype1 | 24 | 49 |
subtype2 | 24 | 60 |
subtype3 | 44 | 57 |
subtype4 | 13 | 21 |
subtype5 | 10 | 44 |
P value = 0.0991 (Fisher's exact test), Q value = 0.23
nPatients | NO | YES |
---|---|---|
ALL | 315 | 9 |
subtype1 | 63 | 3 |
subtype2 | 79 | 1 |
subtype3 | 94 | 1 |
subtype4 | 32 | 0 |
subtype5 | 47 | 4 |
P value = 0.331 (Fisher's exact test), Q value = 0.53
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 2 | 337 | 7 |
subtype1 | 0 | 72 | 1 |
subtype2 | 0 | 83 | 1 |
subtype3 | 2 | 94 | 5 |
subtype4 | 0 | 34 | 0 |
subtype5 | 0 | 54 | 0 |
P value = 0.214 (Fisher's exact test), Q value = 0.4
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 303 | 17 | 1 | 19 |
subtype1 | 66 | 4 | 0 | 3 |
subtype2 | 73 | 2 | 0 | 7 |
subtype3 | 85 | 7 | 1 | 8 |
subtype4 | 27 | 3 | 0 | 1 |
subtype5 | 52 | 1 | 0 | 0 |
P value = 0.00933 (Fisher's exact test), Q value = 0.04
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 155 | 16 | 163 |
subtype1 | 1 | 45 | 0 | 27 |
subtype2 | 0 | 27 | 7 | 44 |
subtype3 | 0 | 43 | 5 | 50 |
subtype4 | 0 | 13 | 3 | 18 |
subtype5 | 1 | 27 | 1 | 24 |
P value = 0.782 (Fisher's exact test), Q value = 0.85
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 16 | 312 |
subtype1 | 5 | 66 |
subtype2 | 4 | 73 |
subtype3 | 3 | 93 |
subtype4 | 2 | 31 |
subtype5 | 2 | 49 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/26874095/LIHC-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/26850637/LIHC-TP.merged_data.txt
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Number of patients = 377
-
Number of clustering approaches = 10
-
Number of selected clinical features = 12
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary clinical features, 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.