This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 10 clinical features across 66 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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5 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.315 (1.00) |
0.853 (1.00) |
0.374 (1.00) |
0.0881 (1.00) |
0.276 (1.00) |
0.111 (1.00) |
0.245 (1.00) |
0.731 (1.00) |
AGE | ANOVA |
0.85 (1.00) |
0.486 (1.00) |
0.341 (1.00) |
0.334 (1.00) |
0.00629 (0.434) |
0.177 (1.00) |
0.412 (1.00) |
0.0345 (1.00) |
NEOPLASM DISEASESTAGE | Chi-square test |
0.478 (1.00) |
0.0599 (1.00) |
0.165 (1.00) |
0.26 (1.00) |
0.146 (1.00) |
0.215 (1.00) |
0.121 (1.00) |
0.48 (1.00) |
PATHOLOGY T STAGE | Chi-square test |
0.476 (1.00) |
0.0264 (1.00) |
0.0771 (1.00) |
0.184 (1.00) |
0.109 (1.00) |
0.204 (1.00) |
0.0675 (1.00) |
0.309 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
0.565 (1.00) |
0.383 (1.00) |
0.113 (1.00) |
0.105 (1.00) |
0.722 (1.00) |
0.387 (1.00) |
0.56 (1.00) |
1 (1.00) |
PATHOLOGY M STAGE | Chi-square test |
0.819 (1.00) |
0.19 (1.00) |
0.167 (1.00) |
0.0805 (1.00) |
0.251 (1.00) |
0.0581 (1.00) |
0.377 (1.00) |
0.205 (1.00) |
GENDER | Fisher's exact test |
0.609 (1.00) |
0.746 (1.00) |
0.366 (1.00) |
0.552 (1.00) |
0.509 (1.00) |
0.29 (1.00) |
0.212 (1.00) |
0.222 (1.00) |
KARNOFSKY PERFORMANCE SCORE | ANOVA |
0.0658 (1.00) |
0.608 (1.00) |
0.264 (1.00) |
0.264 (1.00) |
0.0288 (1.00) |
0.148 (1.00) |
0.0859 (1.00) |
0.142 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.164 (1.00) |
0.0688 (1.00) |
0.0688 (1.00) |
0.297 (1.00) |
0.497 (1.00) |
|||
YEAROFTOBACCOSMOKINGONSET | ANOVA |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 47 | 14 |
P value = 0.315 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 5 | 1 | 37.0 - 92.7 (44.9) |
subtype2 | 46 | 7 | 0.6 - 152.0 (63.8) |
subtype3 | 14 | 0 | 2.5 - 137.1 (68.3) |
P value = 0.85 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 5 | 51.6 (11.7) |
subtype2 | 47 | 52.1 (14.7) |
subtype3 | 14 | 49.6 (14.5) |
P value = 0.478 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 1 | 2 | 2 | 0 |
subtype2 | 13 | 18 | 10 | 6 |
subtype3 | 7 | 5 | 2 | 0 |
P value = 0.476 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 1 | 2 | 2 |
subtype2 | 13 | 18 | 16 |
subtype3 | 7 | 5 | 2 |
P value = 0.565 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 2 | 0 |
subtype2 | 30 | 5 |
subtype3 | 8 | 0 |
P value = 0.819 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 3 | 0 | 1 |
subtype2 | 23 | 2 | 7 |
subtype3 | 8 | 0 | 1 |
P value = 0.609 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 3 | 2 |
subtype2 | 18 | 29 |
subtype3 | 6 | 8 |
P value = 0.0658 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 1 | 90.0 (NA) |
subtype2 | 7 | 85.7 (9.8) |
subtype3 | 3 | 96.7 (5.8) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 35 | 13 |
P value = 0.853 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 18 | 2 | 23.5 - 137.1 (68.3) |
subtype2 | 34 | 5 | 2.5 - 152.0 (65.9) |
subtype3 | 13 | 1 | 0.6 - 98.3 (51.1) |
P value = 0.486 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 18 | 49.7 (13.7) |
subtype2 | 35 | 50.9 (14.0) |
subtype3 | 13 | 55.7 (16.3) |
P value = 0.0599 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 8 | 7 | 3 | 0 |
subtype2 | 6 | 17 | 8 | 4 |
subtype3 | 7 | 1 | 3 | 2 |
P value = 0.0264 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 8 | 7 | 3 |
subtype2 | 6 | 17 | 12 |
subtype3 | 7 | 1 | 5 |
P value = 0.383 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 12 | 0 |
subtype2 | 23 | 4 |
subtype3 | 5 | 1 |
P value = 0.19 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 12 | 0 | 2 |
subtype2 | 17 | 2 | 3 |
subtype3 | 5 | 0 | 4 |
P value = 0.746 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 8 | 10 |
subtype2 | 15 | 20 |
subtype3 | 4 | 9 |
P value = 0.608 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 3 | 93.3 (5.8) |
subtype2 | 3 | 90.0 (10.0) |
subtype3 | 5 | 86.0 (11.4) |
P value = 0.164 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 25.1 (21.9) |
subtype1 | 3 | 12.0 (13.1) |
subtype2 | 6 | 32.7 (26.8) |
subtype3 | 2 | 22.0 (2.8) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 19 | 22 | 15 | 10 |
P value = 0.374 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 19 | 2 | 24.8 - 137.1 (76.9) |
subtype2 | 21 | 1 | 2.5 - 152.0 (62.4) |
subtype3 | 15 | 4 | 16.7 - 114.2 (66.5) |
subtype4 | 10 | 1 | 0.6 - 98.3 (30.1) |
P value = 0.341 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 19 | 47.7 (12.9) |
subtype2 | 22 | 51.8 (15.1) |
subtype3 | 15 | 51.6 (14.3) |
subtype4 | 10 | 58.0 (14.6) |
P value = 0.165 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 7 | 6 | 5 | 1 |
subtype2 | 8 | 11 | 2 | 1 |
subtype3 | 1 | 7 | 5 | 2 |
subtype4 | 5 | 1 | 2 | 2 |
P value = 0.0771 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 7 | 6 | 6 |
subtype2 | 8 | 11 | 3 |
subtype3 | 1 | 7 | 7 |
subtype4 | 5 | 1 | 4 |
P value = 0.113 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 12 | 1 |
subtype2 | 15 | 0 |
subtype3 | 10 | 3 |
subtype4 | 3 | 1 |
P value = 0.167 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 13 | 0 | 2 |
subtype2 | 11 | 1 | 2 |
subtype3 | 7 | 1 | 1 |
subtype4 | 3 | 0 | 4 |
P value = 0.366 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 9 | 10 |
subtype2 | 11 | 11 |
subtype3 | 5 | 10 |
subtype4 | 2 | 8 |
P value = 0.264 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 3 | 93.3 (5.8) |
subtype2 | 3 | 93.3 (11.5) |
subtype3 | 1 | 90.0 (NA) |
subtype4 | 4 | 82.5 (9.6) |
P value = 0.0688 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 25.1 (21.9) |
subtype1 | 3 | 14.3 (11.2) |
subtype2 | 4 | 15.8 (16.5) |
subtype3 | 3 | 50.0 (24.1) |
subtype4 | 1 | 20.0 (NA) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 10 | 10 | 17 | 6 | 23 |
P value = 0.0881 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 10 | 4 | 16.7 - 114.2 (60.1) |
subtype2 | 10 | 1 | 0.6 - 98.3 (26.1) |
subtype3 | 16 | 0 | 3.5 - 152.0 (73.8) |
subtype4 | 6 | 0 | 2.5 - 109.2 (52.3) |
subtype5 | 23 | 3 | 23.8 - 137.1 (73.9) |
P value = 0.334 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 10 | 53.6 (12.7) |
subtype2 | 10 | 55.1 (14.4) |
subtype3 | 17 | 49.2 (14.4) |
subtype4 | 6 | 60.3 (21.1) |
subtype5 | 23 | 48.4 (12.6) |
P value = 0.26 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 1 | 3 | 4 | 2 |
subtype2 | 5 | 2 | 1 | 2 |
subtype3 | 7 | 7 | 2 | 1 |
subtype4 | 0 | 4 | 2 | 0 |
subtype5 | 8 | 9 | 5 | 1 |
P value = 0.184 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 1 | 3 | 6 |
subtype2 | 5 | 2 | 3 |
subtype3 | 7 | 7 | 3 |
subtype4 | 0 | 4 | 2 |
subtype5 | 8 | 9 | 6 |
P value = 0.105 (Chi-square test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 6 | 3 |
subtype2 | 3 | 1 |
subtype3 | 12 | 0 |
subtype4 | 4 | 0 |
subtype5 | 15 | 1 |
P value = 0.0805 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 4 | 1 | 1 |
subtype2 | 2 | 0 | 4 |
subtype3 | 8 | 1 | 2 |
subtype4 | 3 | 0 | 0 |
subtype5 | 17 | 0 | 2 |
P value = 0.552 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 4 | 6 |
subtype2 | 2 | 8 |
subtype3 | 9 | 8 |
subtype4 | 2 | 4 |
subtype5 | 10 | 13 |
P value = 0.264 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 1 | 90.0 (NA) |
subtype2 | 4 | 82.5 (9.6) |
subtype3 | 3 | 93.3 (11.5) |
subtype5 | 3 | 93.3 (5.8) |
P value = 0.0688 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 25.1 (21.9) |
subtype1 | 3 | 50.0 (24.1) |
subtype2 | 1 | 20.0 (NA) |
subtype3 | 4 | 15.8 (16.5) |
subtype5 | 3 | 14.3 (11.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 20 | 24 | 22 |
P value = 0.276 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 19 | 4 | 0.6 - 152.0 (51.1) |
subtype2 | 24 | 2 | 3.5 - 141.7 (83.4) |
subtype3 | 22 | 2 | 11.2 - 114.2 (63.2) |
P value = 0.00629 (ANOVA), Q value = 0.43
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 20 | 58.2 (15.9) |
subtype2 | 24 | 52.2 (13.0) |
subtype3 | 22 | 44.6 (11.1) |
P value = 0.146 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 6 | 4 | 7 | 3 |
subtype2 | 9 | 9 | 3 | 3 |
subtype3 | 6 | 12 | 4 | 0 |
P value = 0.109 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 6 | 4 | 10 |
subtype2 | 9 | 9 | 6 |
subtype3 | 6 | 12 | 4 |
P value = 0.722 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 10 | 2 |
subtype2 | 14 | 2 |
subtype3 | 16 | 1 |
P value = 0.251 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 8 | 1 | 5 |
subtype2 | 15 | 1 | 1 |
subtype3 | 11 | 0 | 3 |
P value = 0.509 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 6 | 14 |
subtype2 | 11 | 13 |
subtype3 | 10 | 12 |
P value = 0.0288 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 5 | 82.0 (8.4) |
subtype2 | 2 | 95.0 (7.1) |
subtype3 | 4 | 95.0 (5.8) |
P value = 0.297 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 25.1 (21.9) |
subtype1 | 3 | 31.7 (14.6) |
subtype2 | 4 | 11.0 (11.3) |
subtype3 | 4 | 34.2 (30.2) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 9 | 57 |
P value = 0.111 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 9 | 2 | 0.6 - 75.8 (28.8) |
subtype2 | 56 | 6 | 2.5 - 152.0 (70.3) |
P value = 0.177 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 9 | 58.4 (15.6) |
subtype2 | 57 | 50.4 (13.9) |
P value = 0.215 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 4 | 1 | 2 | 2 |
subtype2 | 17 | 24 | 12 | 4 |
P value = 0.204 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 4 | 1 | 4 |
subtype2 | 17 | 24 | 16 |
P value = 0.387 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 3 | 1 |
subtype2 | 37 | 4 |
P value = 0.0581 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 2 | 0 | 3 |
subtype2 | 32 | 2 | 6 |
P value = 0.29 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 2 | 7 |
subtype2 | 25 | 32 |
P value = 0.148 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 3 | 80.0 (10.0) |
subtype2 | 8 | 92.5 (7.1) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 10 | 16 | 16 | 10 | 14 |
P value = 0.245 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 10 | 2 | 3.5 - 97.0 (63.4) |
subtype2 | 16 | 0 | 2.5 - 141.7 (55.4) |
subtype3 | 16 | 3 | 23.8 - 137.1 (71.5) |
subtype4 | 10 | 0 | 11.2 - 86.1 (67.2) |
subtype5 | 13 | 3 | 0.6 - 152.0 (52.3) |
P value = 0.412 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 10 | 50.2 (10.7) |
subtype2 | 16 | 52.1 (15.9) |
subtype3 | 16 | 49.1 (15.7) |
subtype4 | 10 | 47.3 (12.1) |
subtype5 | 14 | 57.6 (14.3) |
P value = 0.121 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 5 | 0 | 3 | 2 |
subtype2 | 6 | 8 | 2 | 0 |
subtype3 | 4 | 9 | 1 | 2 |
subtype4 | 2 | 5 | 3 | 0 |
subtype5 | 4 | 3 | 5 | 2 |
P value = 0.0675 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 5 | 0 | 5 |
subtype2 | 6 | 8 | 2 |
subtype3 | 4 | 9 | 3 |
subtype4 | 2 | 5 | 3 |
subtype5 | 4 | 3 | 7 |
P value = 0.56 (Chi-square test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 6 | 1 |
subtype2 | 9 | 0 |
subtype3 | 11 | 2 |
subtype4 | 6 | 0 |
subtype5 | 8 | 2 |
P value = 0.377 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 7 | 1 | 0 |
subtype2 | 5 | 0 | 3 |
subtype3 | 12 | 1 | 1 |
subtype4 | 5 | 0 | 2 |
subtype5 | 5 | 0 | 3 |
P value = 0.212 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 7 | 3 |
subtype2 | 7 | 9 |
subtype3 | 6 | 10 |
subtype4 | 4 | 6 |
subtype5 | 3 | 11 |
P value = 0.0859 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype2 | 3 | 86.7 (5.8) |
subtype3 | 2 | 95.0 (7.1) |
subtype4 | 3 | 96.7 (5.8) |
subtype5 | 3 | 80.0 (10.0) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 8 | 25 | 21 |
P value = 0.731 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 8 | 0.6 - 152.0 (64.0) |
subtype1 | 12 | 2 | 0.6 - 98.3 (41.8) |
subtype2 | 8 | 0 | 2.5 - 141.7 (56.8) |
subtype3 | 24 | 3 | 11.2 - 152.0 (63.2) |
subtype4 | 21 | 3 | 24.8 - 137.1 (76.9) |
P value = 0.0345 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 66 | 51.5 (14.3) |
subtype1 | 12 | 57.6 (16.5) |
subtype2 | 8 | 61.2 (14.3) |
subtype3 | 25 | 47.6 (13.5) |
subtype4 | 21 | 49.0 (11.8) |
P value = 0.48 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
subtype1 | 4 | 2 | 4 | 2 |
subtype2 | 2 | 5 | 0 | 1 |
subtype3 | 7 | 12 | 5 | 1 |
subtype4 | 8 | 6 | 5 | 2 |
P value = 0.309 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 21 | 25 | 20 |
subtype1 | 4 | 2 | 6 |
subtype2 | 2 | 5 | 1 |
subtype3 | 7 | 12 | 6 |
subtype4 | 8 | 6 | 7 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
subtype1 | 6 | 1 |
subtype2 | 4 | 0 |
subtype3 | 17 | 2 |
subtype4 | 13 | 2 |
P value = 0.205 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 34 | 2 | 9 |
subtype1 | 5 | 0 | 3 |
subtype2 | 3 | 1 | 0 |
subtype3 | 11 | 1 | 4 |
subtype4 | 15 | 0 | 2 |
P value = 0.222 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 39 |
subtype1 | 2 | 10 |
subtype2 | 4 | 4 |
subtype3 | 10 | 15 |
subtype4 | 11 | 10 |
P value = 0.142 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 89.1 (9.4) |
subtype1 | 3 | 80.0 (10.0) |
subtype3 | 5 | 92.0 (8.4) |
subtype4 | 3 | 93.3 (5.8) |
P value = 0.497 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 25.1 (21.9) |
subtype1 | 3 | 31.7 (14.6) |
subtype2 | 1 | 1.0 (NA) |
subtype3 | 4 | 34.2 (30.2) |
subtype4 | 3 | 14.3 (11.2) |
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Cluster data file = KICH-TP.mergedcluster.txt
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Clinical data file = KICH-TP.merged_data.txt
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Number of patients = 66
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Number of clustering approaches = 8
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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 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
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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.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.