(primary solid tumor cohort)
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 7 clinical features across 117 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
3 subtypes identified in current cancer cohort by 'CN CNMF'. These subtypes do not correlate to any clinical features.
-
4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
-
CNMF clustering analysis on RPPA data identified 4 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | ANOVA | ANOVA | ANOVA |
CN CNMF |
0.877 (1.00) |
0.493 (1.00) |
0.859 (1.00) |
0.614 (1.00) |
0.803 (1.00) |
0.755 (1.00) |
0.92 (1.00) |
METHLYATION CNMF |
0.484 (1.00) |
0.0426 (1.00) |
0.032 (1.00) |
0.863 (1.00) |
0.763 (1.00) |
0.24 (1.00) |
0.537 (1.00) |
RPPA CNMF subtypes |
0.245 (1.00) |
0.473 (1.00) |
0.633 (1.00) |
0.465 (1.00) |
0.657 (1.00) |
0.955 (1.00) |
0.258 (1.00) |
RPPA cHierClus subtypes |
0.25 (1.00) |
0.164 (1.00) |
0.196 (1.00) |
0.342 (1.00) |
0.677 (1.00) |
0.56 (1.00) |
0.412 (1.00) |
RNAseq CNMF subtypes |
0.641 (1.00) |
0.269 (1.00) |
0.19 (1.00) |
0.412 (1.00) |
0.664 (1.00) |
0.643 (1.00) |
0.0533 (1.00) |
RNAseq cHierClus subtypes |
0.209 (1.00) |
0.958 (1.00) |
0.283 (1.00) |
0.923 (1.00) |
0.688 (1.00) |
0.744 (1.00) |
0.46 (1.00) |
MIRseq CNMF subtypes |
0.478 (1.00) |
0.389 (1.00) |
0.25 (1.00) |
0.559 (1.00) |
0.816 (1.00) |
0.993 (1.00) |
0.463 (1.00) |
MIRseq cHierClus subtypes |
0.878 (1.00) |
0.47 (1.00) |
0.801 (1.00) |
0.715 (1.00) |
0.15 (1.00) |
0.627 (1.00) |
0.385 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 26 | 55 | 33 |
P value = 0.877 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 108 | 29 | 0.4 - 118.9 (6.8) |
subtype1 | 25 | 6 | 0.8 - 75.3 (5.7) |
subtype2 | 51 | 16 | 0.5 - 46.8 (7.2) |
subtype3 | 32 | 7 | 0.4 - 118.9 (6.3) |
P value = 0.493 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 113 | 67.2 (11.1) |
subtype1 | 25 | 69.6 (11.2) |
subtype2 | 55 | 66.7 (12.2) |
subtype3 | 33 | 66.4 (8.8) |
P value = 0.859 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 83 |
subtype1 | 8 | 18 |
subtype2 | 14 | 41 |
subtype3 | 9 | 24 |
P value = 0.614 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 35 | 77.7 (16.6) |
subtype1 | 9 | 82.2 (13.9) |
subtype2 | 17 | 75.3 (18.7) |
subtype3 | 9 | 77.8 (15.6) |
P value = 0.803 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 34.6 (21.7) |
subtype1 | 17 | 34.5 (30.2) |
subtype2 | 29 | 32.8 (19.3) |
subtype3 | 24 | 36.8 (18.0) |
P value = 0.755 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 1991.5 (17.6) |
subtype1 | 14 | 1989.6 (19.6) |
subtype2 | 26 | 1990.7 (18.5) |
subtype3 | 17 | 1994.1 (15.2) |
P value = 0.92 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 108 | 2.6 (1.1) |
subtype1 | 25 | 2.6 (1.1) |
subtype2 | 52 | 2.6 (1.2) |
subtype3 | 31 | 2.7 (1.1) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 29 | 37 | 32 | 19 |
P value = 0.484 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 111 | 30 | 0.4 - 118.9 (6.7) |
subtype1 | 28 | 5 | 0.8 - 118.9 (6.3) |
subtype2 | 36 | 13 | 0.4 - 75.3 (7.2) |
subtype3 | 28 | 5 | 0.7 - 37.8 (6.4) |
subtype4 | 19 | 7 | 0.5 - 46.8 (8.7) |
P value = 0.0426 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 67.3 (11.0) |
subtype1 | 28 | 67.1 (10.5) |
subtype2 | 37 | 68.9 (10.2) |
subtype3 | 32 | 63.1 (12.3) |
subtype4 | 19 | 71.4 (9.2) |
P value = 0.032 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 85 |
subtype1 | 10 | 19 |
subtype2 | 14 | 23 |
subtype3 | 3 | 29 |
subtype4 | 5 | 14 |
P value = 0.863 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 78.1 (16.5) |
subtype1 | 7 | 82.9 (15.0) |
subtype2 | 8 | 77.5 (16.7) |
subtype3 | 16 | 76.2 (18.9) |
subtype4 | 5 | 78.0 (13.0) |
P value = 0.763 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 35.1 (22.1) |
subtype1 | 18 | 31.4 (24.5) |
subtype2 | 26 | 34.2 (20.6) |
subtype3 | 21 | 38.2 (21.7) |
subtype4 | 6 | 39.5 (26.1) |
P value = 0.24 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 58 | 1991.8 (17.6) |
subtype1 | 11 | 1996.0 (15.5) |
subtype2 | 20 | 1987.7 (17.5) |
subtype3 | 17 | 1997.1 (16.3) |
subtype4 | 10 | 1986.2 (20.7) |
P value = 0.537 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 111 | 2.6 (1.1) |
subtype1 | 27 | 2.5 (1.2) |
subtype2 | 34 | 2.6 (1.0) |
subtype3 | 32 | 2.9 (1.3) |
subtype4 | 18 | 2.5 (1.1) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 10 | 14 | 17 |
P value = 0.245 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 52 | 20 | 0.4 - 118.9 (8.3) |
subtype1 | 12 | 4 | 5.7 - 61.9 (10.9) |
subtype2 | 10 | 5 | 1.8 - 100.5 (5.5) |
subtype3 | 13 | 2 | 0.5 - 19.5 (6.6) |
subtype4 | 17 | 9 | 0.4 - 118.9 (14.9) |
P value = 0.473 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 52 | 67.3 (9.8) |
subtype1 | 12 | 63.9 (9.2) |
subtype2 | 10 | 69.5 (9.3) |
subtype3 | 13 | 66.5 (10.2) |
subtype4 | 17 | 69.1 (10.3) |
P value = 0.633 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 32 |
subtype1 | 6 | 6 |
subtype2 | 5 | 5 |
subtype3 | 5 | 9 |
subtype4 | 5 | 12 |
P value = 0.465 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 80.0 (16.7) |
subtype1 | 5 | 88.0 (4.5) |
subtype2 | 1 | 70.0 (NA) |
subtype3 | 1 | 60.0 (NA) |
subtype4 | 4 | 77.5 (25.0) |
P value = 0.657 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 32.1 (17.5) |
subtype1 | 9 | 27.6 (12.4) |
subtype2 | 5 | 28.8 (18.4) |
subtype3 | 6 | 35.2 (20.4) |
subtype4 | 7 | 37.9 (21.6) |
P value = 0.955 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 1990.1 (16.1) |
subtype1 | 6 | 1989.7 (18.5) |
subtype2 | 2 | 1979.0 (11.3) |
subtype3 | 5 | 1992.8 (13.9) |
subtype4 | 8 | 1991.5 (17.9) |
P value = 0.258 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 2.3 (1.1) |
subtype1 | 12 | 2.6 (0.9) |
subtype2 | 8 | 1.9 (0.8) |
subtype3 | 14 | 2.1 (1.1) |
subtype4 | 14 | 2.6 (1.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 14 | 17 | 22 |
P value = 0.25 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 52 | 20 | 0.4 - 118.9 (8.3) |
subtype1 | 14 | 5 | 1.9 - 61.9 (8.3) |
subtype2 | 17 | 10 | 0.4 - 118.9 (8.2) |
subtype3 | 21 | 5 | 0.5 - 100.5 (7.7) |
P value = 0.164 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 52 | 67.3 (9.8) |
subtype1 | 14 | 63.5 (9.6) |
subtype2 | 17 | 70.2 (9.0) |
subtype3 | 21 | 67.5 (10.2) |
P value = 0.196 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 32 |
subtype1 | 8 | 6 |
subtype2 | 7 | 10 |
subtype3 | 6 | 16 |
P value = 0.342 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 80.0 (16.7) |
subtype1 | 4 | 90.0 (0.0) |
subtype2 | 4 | 72.5 (23.6) |
subtype3 | 3 | 76.7 (15.3) |
P value = 0.677 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 32.1 (17.5) |
subtype1 | 9 | 30.4 (15.6) |
subtype2 | 8 | 29.1 (18.5) |
subtype3 | 10 | 36.1 (19.4) |
P value = 0.56 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 1990.1 (16.1) |
subtype1 | 4 | 1997.8 (13.0) |
subtype2 | 9 | 1987.0 (16.8) |
subtype3 | 8 | 1989.8 (17.2) |
P value = 0.412 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 2.3 (1.1) |
subtype1 | 13 | 2.3 (0.9) |
subtype2 | 14 | 2.6 (1.1) |
subtype3 | 21 | 2.1 (1.2) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 37 | 18 | 25 | 10 |
P value = 0.641 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 84 | 25 | 0.4 - 118.9 (7.2) |
subtype1 | 32 | 9 | 0.5 - 100.5 (7.1) |
subtype2 | 18 | 8 | 4.1 - 118.9 (6.7) |
subtype3 | 25 | 6 | 0.4 - 75.3 (8.2) |
subtype4 | 9 | 2 | 1.8 - 11.1 (5.1) |
P value = 0.269 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 66.4 (11.6) |
subtype1 | 36 | 66.5 (12.2) |
subtype2 | 18 | 62.7 (9.7) |
subtype3 | 25 | 66.9 (12.1) |
subtype4 | 10 | 71.6 (9.9) |
P value = 0.19 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 63 |
subtype1 | 8 | 29 |
subtype2 | 4 | 14 |
subtype3 | 10 | 15 |
subtype4 | 5 | 5 |
P value = 0.412 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 26 | 77.7 (17.7) |
subtype1 | 12 | 75.8 (17.8) |
subtype2 | 7 | 85.7 (7.9) |
subtype3 | 6 | 73.3 (25.8) |
subtype4 | 1 | 70.0 (NA) |
P value = 0.664 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 51 | 34.6 (22.7) |
subtype1 | 15 | 40.8 (30.9) |
subtype2 | 15 | 31.6 (19.5) |
subtype3 | 16 | 33.2 (19.5) |
subtype4 | 5 | 30.0 (12.2) |
P value = 0.643 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1990.6 (18.5) |
subtype1 | 14 | 1988.9 (20.8) |
subtype2 | 9 | 1997.4 (17.3) |
subtype3 | 14 | 1987.6 (17.6) |
subtype4 | 5 | 1991.8 (18.9) |
P value = 0.0533 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 2.5 (1.1) |
subtype1 | 34 | 2.2 (1.2) |
subtype2 | 16 | 3.0 (0.8) |
subtype3 | 24 | 2.7 (1.0) |
subtype4 | 10 | 2.1 (1.1) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 25 | 44 | 21 |
P value = 0.209 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 84 | 25 | 0.4 - 118.9 (7.2) |
subtype1 | 25 | 6 | 0.4 - 75.3 (8.3) |
subtype2 | 39 | 10 | 0.5 - 100.5 (6.7) |
subtype3 | 20 | 9 | 1.8 - 118.9 (5.9) |
P value = 0.958 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 66.4 (11.6) |
subtype1 | 25 | 67.0 (12.0) |
subtype2 | 43 | 66.2 (11.8) |
subtype3 | 21 | 66.2 (11.1) |
P value = 0.283 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 27 | 63 |
subtype1 | 10 | 15 |
subtype2 | 10 | 34 |
subtype3 | 7 | 14 |
P value = 0.923 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 26 | 77.7 (17.7) |
subtype1 | 7 | 75.7 (24.4) |
subtype2 | 14 | 77.9 (17.2) |
subtype3 | 5 | 80.0 (10.0) |
P value = 0.688 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 51 | 34.6 (22.7) |
subtype1 | 16 | 33.5 (19.5) |
subtype2 | 20 | 38.0 (30.3) |
subtype3 | 15 | 31.4 (13.0) |
P value = 0.744 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 1990.6 (18.5) |
subtype1 | 14 | 1987.6 (17.6) |
subtype2 | 18 | 1991.6 (20.0) |
subtype3 | 10 | 1993.2 (18.4) |
P value = 0.46 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 2.5 (1.1) |
subtype1 | 24 | 2.7 (1.0) |
subtype2 | 41 | 2.3 (1.2) |
subtype3 | 19 | 2.6 (1.0) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 24 | 57 | 29 |
P value = 0.478 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 104 | 30 | 0.4 - 118.9 (7.0) |
subtype1 | 20 | 3 | 0.8 - 118.9 (6.4) |
subtype2 | 55 | 20 | 0.4 - 61.9 (7.0) |
subtype3 | 29 | 7 | 0.5 - 100.5 (8.1) |
P value = 0.389 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 109 | 67.3 (11.0) |
subtype1 | 23 | 68.4 (12.1) |
subtype2 | 57 | 65.9 (10.9) |
subtype3 | 29 | 69.1 (10.2) |
P value = 0.25 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 79 |
subtype1 | 4 | 20 |
subtype2 | 16 | 41 |
subtype3 | 11 | 18 |
P value = 0.559 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 76.8 (17.4) |
subtype1 | 6 | 83.3 (10.3) |
subtype2 | 20 | 74.5 (19.9) |
subtype3 | 5 | 78.0 (13.0) |
P value = 0.816 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 35.6 (22.5) |
subtype1 | 14 | 32.1 (27.0) |
subtype2 | 35 | 36.3 (19.3) |
subtype3 | 16 | 36.9 (26.1) |
P value = 0.993 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 1991.4 (17.8) |
subtype1 | 13 | 1990.9 (23.0) |
subtype2 | 24 | 1991.7 (16.3) |
subtype3 | 17 | 1991.4 (16.5) |
P value = 0.463 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 104 | 2.6 (1.1) |
subtype1 | 23 | 2.6 (1.3) |
subtype2 | 54 | 2.5 (1.0) |
subtype3 | 27 | 2.8 (1.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 23 | 75 | 12 |
P value = 0.878 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 104 | 30 | 0.4 - 118.9 (7.0) |
subtype1 | 19 | 4 | 1.5 - 118.9 (6.7) |
subtype2 | 73 | 22 | 0.4 - 100.5 (7.3) |
subtype3 | 12 | 4 | 0.8 - 46.8 (5.6) |
P value = 0.47 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 109 | 67.3 (11.0) |
subtype1 | 22 | 69.5 (12.4) |
subtype2 | 75 | 66.4 (11.0) |
subtype3 | 12 | 68.5 (7.6) |
P value = 0.801 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 79 |
subtype1 | 5 | 18 |
subtype2 | 23 | 52 |
subtype3 | 3 | 9 |
P value = 0.715 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 76.8 (17.4) |
subtype1 | 4 | 80.0 (11.5) |
subtype2 | 24 | 75.4 (18.9) |
subtype3 | 3 | 83.3 (11.5) |
P value = 0.15 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 65 | 35.6 (22.5) |
subtype1 | 13 | 28.5 (24.2) |
subtype2 | 43 | 35.2 (19.8) |
subtype3 | 9 | 47.4 (29.8) |
P value = 0.627 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 1991.4 (17.8) |
subtype1 | 12 | 1987.2 (22.3) |
subtype2 | 33 | 1992.2 (17.2) |
subtype3 | 9 | 1994.2 (13.8) |
P value = 0.385 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 104 | 2.6 (1.1) |
subtype1 | 22 | 2.5 (1.3) |
subtype2 | 70 | 2.6 (1.1) |
subtype3 | 12 | 3.0 (1.0) |
-
Cluster data file = BLCA-TP.mergedcluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 117
-
Number of clustering approaches = 8
-
Number of selected clinical features = 7
-
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.