This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 7 different clustering approaches and 10 clinical features across 283 patients, 10 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'GENDER', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'GENDER', and 'PATHOLOGY.N'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that correlate to 'Time to Death', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.N'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
mRNA CNMF subtypes |
mRNA cHierClus subtypes |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRseq CNMF subtypes |
MIRseq cHierClus subtypes |
Time to Death | logrank test | 0.337 | 0.671 | 0.00488 | 0.00509 | 2.87e-05 | 0.657 | 0.844 |
AGE | ANOVA | 0.477 | 0.557 | 0.448 | 0.117 | 0.197 | 0.193 | 0.0506 |
GENDER | Fisher's exact test | 0.272 | 0.383 | 0.014 | 2.22e-05 | 6.45e-06 | 0.0866 | 0.466 |
KARNOFSKY PERFORMANCE SCORE | ANOVA | 0.679 | 0.631 | 0.576 | 0.43 | |||
HISTOLOGICAL TYPE | Chi-square test | 0.3 | 0.274 | 0.191 | 0.112 | 0.000331 | 0.0827 | 0.0796 |
PATHOLOGY T | Chi-square test | 0.489 | 0.479 | 0.755 | 0.224 | 0.0898 | 0.682 | 0.545 |
PATHOLOGY N | Chi-square test | 0.572 | 0.651 | 0.574 | 0.0264 | 0.00175 | 0.509 | 0.599 |
PATHOLOGICSPREAD(M) | Chi-square test | 0.504 | 1 | 0.435 | 0.421 | 0.488 | 0.144 | 0.0639 |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test | 1 | 1 | 0.0255 | 1 | 0.661 | 0.552 | 0.821 |
NEOADJUVANT THERAPY | Fisher's exact test | 0.921 | 1 | 0.296 | 0.576 | 0.166 | 1 | 0.682 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 5 | 9 | 12 | 6 |
P value = 0.337 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 31 | 4 | 0.5 - 56.8 (8.3) |
subtype1 | 4 | 0 | 6.0 - 48.6 (9.7) |
subtype2 | 9 | 1 | 4.0 - 56.8 (8.3) |
subtype3 | 12 | 1 | 0.5 - 37.0 (3.3) |
subtype4 | 6 | 2 | 2.0 - 45.2 (30.9) |
P value = 0.477 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 65.7 (10.8) |
subtype1 | 4 | 58.5 (15.5) |
subtype2 | 9 | 65.0 (9.1) |
subtype3 | 12 | 67.1 (11.1) |
subtype4 | 5 | 69.4 (9.0) |
P value = 0.272 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 18 |
subtype1 | 2 | 3 |
subtype2 | 6 | 3 |
subtype3 | 3 | 9 |
subtype4 | 3 | 3 |
P value = 0.3 (Chi-square test)
nPatients | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG CLEAR CELL ADENOCARCINOMA |
---|---|---|---|
ALL | 1 | 30 | 1 |
subtype1 | 0 | 4 | 1 |
subtype2 | 0 | 9 | 0 |
subtype3 | 1 | 11 | 0 |
subtype4 | 0 | 6 | 0 |
P value = 0.489 (Chi-square test)
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 12 | 19 | 1 |
subtype1 | 3 | 2 | 0 |
subtype2 | 4 | 4 | 1 |
subtype3 | 4 | 8 | 0 |
subtype4 | 1 | 5 | 0 |
P value = 0.572 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 23 | 4 | 4 |
subtype1 | 3 | 1 | 1 |
subtype2 | 8 | 1 | 0 |
subtype3 | 9 | 1 | 1 |
subtype4 | 3 | 1 | 2 |
P value = 0.504 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 30 | 2 |
subtype1 | 4 | 1 |
subtype2 | 9 | 0 |
subtype3 | 11 | 1 |
subtype4 | 6 | 0 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 31 | 1 |
subtype1 | 5 | 0 |
subtype2 | 9 | 0 |
subtype3 | 11 | 1 |
subtype4 | 6 | 0 |
P value = 0.921 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 26 | 6 |
subtype1 | 4 | 1 |
subtype2 | 8 | 1 |
subtype3 | 9 | 3 |
subtype4 | 5 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 7 | 13 | 12 |
P value = 0.671 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 31 | 4 | 0.5 - 56.8 (8.3) |
subtype1 | 7 | 2 | 2.0 - 48.6 (38.7) |
subtype2 | 13 | 1 | 0.5 - 37.0 (3.4) |
subtype3 | 11 | 1 | 4.0 - 56.8 (8.1) |
P value = 0.557 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 65.7 (10.8) |
subtype1 | 5 | 69.4 (9.0) |
subtype2 | 13 | 66.5 (10.9) |
subtype3 | 12 | 63.3 (11.6) |
P value = 0.383 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 14 | 18 |
subtype1 | 3 | 4 |
subtype2 | 4 | 9 |
subtype3 | 7 | 5 |
P value = 0.274 (Chi-square test)
nPatients | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG CLEAR CELL ADENOCARCINOMA |
---|---|---|---|
ALL | 1 | 30 | 1 |
subtype1 | 0 | 6 | 1 |
subtype2 | 1 | 12 | 0 |
subtype3 | 0 | 12 | 0 |
P value = 0.479 (Chi-square test)
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 12 | 19 | 1 |
subtype1 | 2 | 5 | 0 |
subtype2 | 4 | 9 | 0 |
subtype3 | 6 | 5 | 1 |
P value = 0.651 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 23 | 4 | 4 |
subtype1 | 4 | 1 | 2 |
subtype2 | 10 | 1 | 1 |
subtype3 | 9 | 2 | 1 |
P value = 1 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 30 | 2 |
subtype1 | 7 | 0 |
subtype2 | 12 | 1 |
subtype3 | 11 | 1 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 31 | 1 |
subtype1 | 7 | 0 |
subtype2 | 12 | 1 |
subtype3 | 12 | 0 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 26 | 6 |
subtype1 | 6 | 1 |
subtype2 | 10 | 3 |
subtype3 | 10 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 52 | 60 | 52 | 52 |
P value = 0.00488 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 188 | 60 | 0.0 - 224.0 (11.6) |
subtype1 | 44 | 10 | 0.1 - 224.0 (11.6) |
subtype2 | 53 | 23 | 0.1 - 88.1 (15.0) |
subtype3 | 45 | 11 | 0.0 - 77.9 (5.4) |
subtype4 | 46 | 16 | 0.0 - 71.5 (12.8) |
P value = 0.448 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 188 | 65.3 (9.8) |
subtype1 | 42 | 67.5 (7.8) |
subtype2 | 54 | 64.7 (9.1) |
subtype3 | 47 | 64.8 (10.5) |
subtype4 | 45 | 64.5 (11.5) |
P value = 0.014 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 101 | 115 |
subtype1 | 17 | 35 |
subtype2 | 37 | 23 |
subtype3 | 26 | 26 |
subtype4 | 21 | 31 |
P value = 0.679 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 18 | 71.1 (34.3) |
subtype1 | 7 | 80.0 (35.6) |
subtype2 | 4 | 62.5 (41.9) |
subtype3 | 5 | 78.0 (14.8) |
subtype4 | 2 | 40.0 (56.6) |
P value = 0.191 (Chi-square test)
nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 5 | 49 | 132 | 3 | 9 | 1 | 2 | 2 | 9 | 1 | 3 |
subtype1 | 3 | 9 | 28 | 1 | 6 | 0 | 1 | 2 | 1 | 0 | 1 |
subtype2 | 1 | 17 | 35 | 0 | 1 | 0 | 0 | 0 | 3 | 1 | 2 |
subtype3 | 0 | 14 | 32 | 1 | 1 | 0 | 1 | 0 | 3 | 0 | 0 |
subtype4 | 1 | 9 | 37 | 1 | 1 | 1 | 0 | 0 | 2 | 0 | 0 |
P value = 0.755 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 60 | 125 | 17 | 12 |
subtype1 | 18 | 26 | 5 | 2 |
subtype2 | 14 | 38 | 4 | 4 |
subtype3 | 13 | 30 | 4 | 5 |
subtype4 | 15 | 31 | 4 | 1 |
P value = 0.574 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 125 | 44 | 42 |
subtype1 | 33 | 9 | 9 |
subtype2 | 38 | 11 | 10 |
subtype3 | 28 | 14 | 9 |
subtype4 | 26 | 10 | 14 |
P value = 0.435 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 139 | 10 | 61 |
subtype1 | 35 | 0 | 14 |
subtype2 | 41 | 4 | 14 |
subtype3 | 29 | 4 | 17 |
subtype4 | 34 | 2 | 16 |
P value = 0.0255 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 207 | 9 |
subtype1 | 52 | 0 |
subtype2 | 58 | 2 |
subtype3 | 51 | 1 |
subtype4 | 46 | 6 |
P value = 0.296 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 185 | 31 |
subtype1 | 41 | 11 |
subtype2 | 55 | 5 |
subtype3 | 45 | 7 |
subtype4 | 44 | 8 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 88 | 68 | 84 |
P value = 0.00509 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 214 | 75 | 0.0 - 224.0 (15.0) |
subtype1 | 77 | 19 | 0.1 - 224.0 (13.9) |
subtype2 | 60 | 25 | 0.0 - 77.9 (11.0) |
subtype3 | 77 | 31 | 0.0 - 88.1 (18.3) |
P value = 0.117 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 214 | 65.5 (9.7) |
subtype1 | 79 | 67.1 (8.5) |
subtype2 | 59 | 63.7 (11.3) |
subtype3 | 76 | 65.1 (9.5) |
P value = 2.22e-05 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 110 | 130 |
subtype1 | 26 | 62 |
subtype2 | 30 | 38 |
subtype3 | 54 | 30 |
P value = 0.631 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 18 | 69.4 (39.0) |
subtype1 | 8 | 71.2 (44.2) |
subtype2 | 7 | 60.0 (42.0) |
subtype3 | 3 | 86.7 (5.8) |
P value = 0.112 (Chi-square test)
nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 3 | 52 | 156 | 3 | 8 | 2 | 2 | 2 | 9 | 1 | 2 |
subtype1 | 2 | 17 | 56 | 3 | 6 | 0 | 1 | 1 | 2 | 0 | 0 |
subtype2 | 0 | 11 | 51 | 0 | 2 | 1 | 1 | 0 | 2 | 0 | 0 |
subtype3 | 1 | 24 | 49 | 0 | 0 | 1 | 0 | 1 | 5 | 1 | 2 |
P value = 0.224 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 61 | 144 | 21 | 13 |
subtype1 | 31 | 47 | 6 | 3 |
subtype2 | 14 | 42 | 7 | 5 |
subtype3 | 16 | 55 | 8 | 5 |
P value = 0.0264 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 136 | 53 | 46 |
subtype1 | 60 | 15 | 10 |
subtype2 | 30 | 19 | 18 |
subtype3 | 46 | 19 | 18 |
P value = 0.421 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 176 | 12 | 46 |
subtype1 | 64 | 4 | 16 |
subtype2 | 53 | 1 | 14 |
subtype3 | 59 | 7 | 16 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 229 | 11 |
subtype1 | 84 | 4 |
subtype2 | 65 | 3 |
subtype3 | 80 | 4 |
P value = 0.576 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 203 | 37 |
subtype1 | 75 | 13 |
subtype2 | 55 | 13 |
subtype3 | 73 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 25 | 12 | 49 | 23 | 56 | 75 |
P value = 2.87e-05 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 214 | 75 | 0.0 - 224.0 (15.0) |
subtype1 | 25 | 15 | 0.1 - 45.2 (15.1) |
subtype2 | 10 | 3 | 0.0 - 48.5 (16.2) |
subtype3 | 43 | 12 | 0.1 - 83.8 (16.4) |
subtype4 | 21 | 9 | 0.5 - 104.2 (32.1) |
subtype5 | 48 | 18 | 0.0 - 77.9 (10.0) |
subtype6 | 67 | 18 | 0.1 - 224.0 (13.7) |
P value = 0.197 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 214 | 65.5 (9.7) |
subtype1 | 24 | 66.6 (9.3) |
subtype2 | 10 | 68.1 (10.8) |
subtype3 | 43 | 62.7 (9.6) |
subtype4 | 22 | 67.9 (7.1) |
subtype5 | 48 | 64.2 (11.7) |
subtype6 | 67 | 66.5 (8.8) |
P value = 6.45e-06 (Chi-square test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 110 | 130 |
subtype1 | 15 | 10 |
subtype2 | 6 | 6 |
subtype3 | 31 | 18 |
subtype4 | 17 | 6 |
subtype5 | 24 | 32 |
subtype6 | 17 | 58 |
P value = 0.576 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 18 | 69.4 (39.0) |
subtype3 | 4 | 85.0 (5.8) |
subtype4 | 1 | 90.0 (NA) |
subtype5 | 6 | 56.7 (45.0) |
subtype6 | 7 | 68.6 (47.1) |
P value = 0.000331 (Chi-square test)
nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 3 | 52 | 156 | 3 | 8 | 2 | 2 | 2 | 9 | 1 | 2 |
subtype1 | 0 | 10 | 11 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 |
subtype2 | 0 | 3 | 6 | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
subtype3 | 1 | 8 | 36 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | 0 |
subtype4 | 0 | 10 | 11 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 |
subtype5 | 0 | 9 | 41 | 0 | 1 | 1 | 1 | 0 | 3 | 0 | 0 |
subtype6 | 2 | 12 | 51 | 1 | 6 | 0 | 1 | 1 | 1 | 0 | 0 |
P value = 0.0898 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 61 | 144 | 21 | 13 |
subtype1 | 2 | 18 | 3 | 2 |
subtype2 | 3 | 5 | 3 | 1 |
subtype3 | 13 | 32 | 3 | 1 |
subtype4 | 4 | 15 | 1 | 3 |
subtype5 | 11 | 34 | 7 | 4 |
subtype6 | 28 | 40 | 4 | 2 |
P value = 0.00175 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 136 | 53 | 46 |
subtype1 | 6 | 10 | 9 |
subtype2 | 7 | 4 | 1 |
subtype3 | 32 | 5 | 11 |
subtype4 | 17 | 5 | 1 |
subtype5 | 25 | 15 | 15 |
subtype6 | 49 | 14 | 9 |
P value = 0.488 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 176 | 12 | 46 |
subtype1 | 19 | 2 | 4 |
subtype2 | 9 | 1 | 2 |
subtype3 | 30 | 3 | 14 |
subtype4 | 19 | 2 | 2 |
subtype5 | 47 | 1 | 8 |
subtype6 | 52 | 3 | 16 |
P value = 0.661 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 229 | 11 |
subtype1 | 23 | 2 |
subtype2 | 12 | 0 |
subtype3 | 47 | 2 |
subtype4 | 23 | 0 |
subtype5 | 54 | 2 |
subtype6 | 70 | 5 |
P value = 0.166 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 203 | 37 |
subtype1 | 21 | 4 |
subtype2 | 9 | 3 |
subtype3 | 44 | 5 |
subtype4 | 23 | 0 |
subtype5 | 44 | 12 |
subtype6 | 62 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 39 | 29 | 32 |
P value = 0.657 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 30 | 0.0 - 85.3 (17.4) |
subtype1 | 31 | 14 | 0.0 - 49.0 (25.0) |
subtype2 | 25 | 7 | 0.0 - 60.0 (13.2) |
subtype3 | 29 | 9 | 0.5 - 85.3 (14.1) |
P value = 0.193 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.3 (9.6) |
subtype1 | 35 | 64.5 (8.8) |
subtype2 | 21 | 63.2 (10.7) |
subtype3 | 28 | 67.9 (9.3) |
P value = 0.0866 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 55 |
subtype1 | 16 | 23 |
subtype2 | 18 | 11 |
subtype3 | 11 | 21 |
P value = 0.0827 (Chi-square test)
nPatients | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
---|---|---|---|---|---|---|
ALL | 20 | 72 | 2 | 1 | 3 | 2 |
subtype1 | 13 | 25 | 0 | 0 | 1 | 0 |
subtype2 | 3 | 23 | 1 | 0 | 0 | 2 |
subtype3 | 4 | 24 | 1 | 1 | 2 | 0 |
P value = 0.682 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 27 | 62 | 8 | 3 |
subtype1 | 10 | 24 | 3 | 2 |
subtype2 | 7 | 18 | 4 | 0 |
subtype3 | 10 | 20 | 1 | 1 |
P value = 0.509 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 58 | 22 | 18 |
subtype1 | 19 | 9 | 10 |
subtype2 | 18 | 7 | 4 |
subtype3 | 21 | 6 | 4 |
P value = 0.144 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 81 | 5 | 13 |
subtype1 | 32 | 2 | 4 |
subtype2 | 22 | 0 | 7 |
subtype3 | 27 | 3 | 2 |
P value = 0.552 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 96 | 4 |
subtype1 | 37 | 2 |
subtype2 | 29 | 0 |
subtype3 | 30 | 2 |
P value = 1 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 88 | 12 |
subtype1 | 34 | 5 |
subtype2 | 26 | 3 |
subtype3 | 28 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 40 | 31 | 29 |
P value = 0.844 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 30 | 0.0 - 85.3 (17.4) |
subtype1 | 36 | 11 | 0.0 - 85.3 (8.4) |
subtype2 | 27 | 10 | 0.6 - 76.2 (15.2) |
subtype3 | 22 | 9 | 0.0 - 47.6 (27.5) |
P value = 0.0506 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.3 (9.6) |
subtype1 | 31 | 62.4 (9.5) |
subtype2 | 28 | 68.4 (8.7) |
subtype3 | 25 | 65.5 (9.7) |
P value = 0.466 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 55 |
subtype1 | 20 | 20 |
subtype2 | 11 | 20 |
subtype3 | 14 | 15 |
P value = 0.43 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 6 | 75.0 (37.3) |
subtype1 | 3 | 90.0 (0.0) |
subtype2 | 3 | 60.0 (52.9) |
P value = 0.0796 (Chi-square test)
nPatients | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
---|---|---|---|---|---|---|
ALL | 20 | 72 | 2 | 1 | 3 | 2 |
subtype1 | 4 | 33 | 1 | 0 | 0 | 2 |
subtype2 | 5 | 22 | 1 | 1 | 2 | 0 |
subtype3 | 11 | 17 | 0 | 0 | 1 | 0 |
P value = 0.545 (Chi-square test)
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 27 | 62 | 8 | 3 |
subtype1 | 9 | 27 | 4 | 0 |
subtype2 | 10 | 19 | 1 | 1 |
subtype3 | 8 | 16 | 3 | 2 |
P value = 0.599 (Chi-square test)
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 58 | 22 | 18 |
subtype1 | 23 | 10 | 7 |
subtype2 | 21 | 5 | 4 |
subtype3 | 14 | 7 | 7 |
P value = 0.0639 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 81 | 5 | 13 |
subtype1 | 31 | 0 | 9 |
subtype2 | 27 | 3 | 1 |
subtype3 | 23 | 2 | 3 |
P value = 0.821 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 96 | 4 |
subtype1 | 39 | 1 |
subtype2 | 29 | 2 |
subtype3 | 28 | 1 |
P value = 0.682 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 88 | 12 |
subtype1 | 34 | 6 |
subtype2 | 27 | 4 |
subtype3 | 27 | 2 |
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Cluster data file = LUAD.mergedcluster.txt
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Clinical data file = LUAD.clin.merged.picked.txt
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Number of patients = 283
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Number of clustering approaches = 7
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Number of selected clinical features = 10
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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 continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.