(Regional_LN 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 116 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
4 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. 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 5 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | Chi-square test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.448 (1.00) |
0.0195 (0.899) |
0.566 (1.00) |
0.555 (1.00) |
0.864 (1.00) |
0.27 (1.00) |
|
METHLYATION CNMF |
0.0241 (1.00) |
0.0625 (1.00) |
0.384 (1.00) |
0.694 (1.00) |
0.719 (1.00) |
0.357 (1.00) |
|
RPPA CNMF subtypes |
0.466 (1.00) |
0.104 (1.00) |
0.212 (1.00) |
0.818 (1.00) |
0.424 (1.00) |
0.512 (1.00) |
|
RPPA cHierClus subtypes |
0.0406 (1.00) |
0.856 (1.00) |
0.0741 (1.00) |
0.489 (1.00) |
0.177 (1.00) |
0.0129 (0.606) |
|
RNAseq CNMF subtypes |
0.109 (1.00) |
0.387 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.432 (1.00) |
0.113 (1.00) |
|
RNAseq cHierClus subtypes |
0.636 (1.00) |
0.0724 (1.00) |
0.671 (1.00) |
0.558 (1.00) |
0.531 (1.00) |
0.102 (1.00) |
|
MIRSEQ CNMF |
0.304 (1.00) |
0.0367 (1.00) |
0.496 (1.00) |
0.29 (1.00) |
0.854 (1.00) |
0.00574 (0.275) |
|
MIRSEQ CHIERARCHICAL |
0.275 (1.00) |
0.305 (1.00) |
0.158 (1.00) |
0.526 (1.00) |
0.296 (1.00) |
0.0351 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 30 | 18 | 38 | 26 |
P value = 0.448 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 59 | 32 | 1.0 - 98.8 (13.0) |
subtype1 | 17 | 10 | 1.1 - 48.8 (11.1) |
subtype2 | 13 | 8 | 1.1 - 51.1 (28.6) |
subtype3 | 19 | 10 | 4.0 - 98.8 (12.2) |
subtype4 | 10 | 4 | 1.0 - 25.3 (8.9) |
P value = 0.0195 (ANOVA), Q value = 0.9
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 112 | 55.4 (16.4) |
subtype1 | 30 | 61.3 (17.2) |
subtype2 | 18 | 46.1 (16.0) |
subtype3 | 38 | 55.6 (16.0) |
subtype4 | 26 | 54.9 (13.9) |
P value = 0.566 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 77 |
subtype1 | 11 | 19 |
subtype2 | 4 | 14 |
subtype3 | 10 | 28 |
subtype4 | 10 | 16 |
P value = 0.555 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 98 | 1 | 2 | 1 |
subtype1 | 25 | 0 | 0 | 1 |
subtype2 | 16 | 0 | 0 | 0 |
subtype3 | 35 | 0 | 1 | 0 |
subtype4 | 22 | 1 | 1 | 0 |
P value = 0.864 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 61 | 1 | 3 | 10 | 1 | 3 | 8 | 1 | 13 | 2 |
subtype1 | 17 | 0 | 1 | 2 | 0 | 0 | 2 | 1 | 3 | 1 |
subtype2 | 8 | 0 | 1 | 3 | 0 | 0 | 1 | 0 | 2 | 1 |
subtype3 | 23 | 1 | 1 | 2 | 0 | 1 | 3 | 0 | 5 | 0 |
subtype4 | 13 | 0 | 0 | 3 | 1 | 2 | 2 | 0 | 3 | 0 |
P value = 0.27 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 13 | 5 | 5 | 2 | 4 | 3 | 10 | 18 | 3 |
subtype1 | 0 | 1 | 2 | 3 | 3 | 1 | 4 | 2 | 0 | 1 | 3 | 4 | 1 |
subtype2 | 1 | 1 | 1 | 2 | 2 | 1 | 0 | 0 | 0 | 1 | 2 | 4 | 0 |
subtype3 | 0 | 10 | 2 | 3 | 3 | 3 | 1 | 0 | 1 | 1 | 3 | 7 | 1 |
subtype4 | 0 | 3 | 2 | 3 | 5 | 0 | 0 | 0 | 3 | 0 | 2 | 3 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 20 | 40 | 27 | 29 |
P value = 0.0241 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 63 | 33 | 0.2 - 98.8 (12.0) |
subtype1 | 12 | 5 | 0.2 - 38.6 (15.5) |
subtype2 | 21 | 10 | 2.9 - 98.8 (22.4) |
subtype3 | 15 | 12 | 1.1 - 48.8 (8.8) |
subtype4 | 15 | 6 | 0.2 - 51.1 (10.0) |
P value = 0.0625 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 116 | 55.1 (16.2) |
subtype1 | 20 | 51.4 (16.8) |
subtype2 | 40 | 53.2 (14.3) |
subtype3 | 27 | 53.4 (17.4) |
subtype4 | 29 | 62.1 (16.0) |
P value = 0.384 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 79 |
subtype1 | 4 | 16 |
subtype2 | 11 | 29 |
subtype3 | 11 | 16 |
subtype4 | 11 | 18 |
P value = 0.694 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 102 | 1 | 2 | 1 |
subtype1 | 17 | 0 | 0 | 0 |
subtype2 | 35 | 0 | 1 | 1 |
subtype3 | 25 | 1 | 0 | 0 |
subtype4 | 25 | 0 | 1 | 0 |
P value = 0.719 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 61 | 1 | 4 | 10 | 1 | 3 | 9 | 1 | 15 | 2 |
subtype1 | 10 | 0 | 1 | 2 | 0 | 0 | 1 | 0 | 3 | 1 |
subtype2 | 22 | 1 | 1 | 4 | 0 | 0 | 3 | 1 | 5 | 0 |
subtype3 | 15 | 0 | 2 | 2 | 0 | 1 | 4 | 0 | 1 | 1 |
subtype4 | 14 | 0 | 0 | 2 | 1 | 2 | 1 | 0 | 6 | 0 |
P value = 0.357 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 13 | 5 | 5 | 2 | 5 | 3 | 11 | 20 | 3 |
subtype1 | 1 | 1 | 0 | 2 | 2 | 1 | 2 | 1 | 0 | 1 | 2 | 4 | 0 |
subtype2 | 0 | 10 | 1 | 4 | 3 | 3 | 0 | 0 | 2 | 0 | 5 | 6 | 2 |
subtype3 | 0 | 2 | 2 | 3 | 6 | 0 | 1 | 0 | 2 | 1 | 3 | 3 | 1 |
subtype4 | 0 | 2 | 4 | 2 | 2 | 1 | 2 | 1 | 1 | 1 | 1 | 7 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 12 | 24 | 15 | 14 | 15 |
P value = 0.466 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 40 | 22 | 1.1 - 98.8 (13.5) |
subtype1 | 10 | 4 | 5.1 - 84.7 (16.3) |
subtype2 | 8 | 6 | 4.2 - 42.8 (13.2) |
subtype3 | 8 | 2 | 1.1 - 98.8 (10.8) |
subtype4 | 10 | 7 | 1.1 - 78.4 (15.0) |
subtype5 | 4 | 3 | 4.3 - 35.8 (9.0) |
P value = 0.104 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 56.5 (15.9) |
subtype1 | 12 | 52.8 (16.9) |
subtype2 | 24 | 52.9 (17.3) |
subtype3 | 15 | 62.2 (13.3) |
subtype4 | 14 | 63.9 (10.1) |
subtype5 | 15 | 52.8 (17.4) |
P value = 0.212 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 51 |
subtype1 | 3 | 9 |
subtype2 | 8 | 16 |
subtype3 | 9 | 6 |
subtype4 | 3 | 11 |
subtype5 | 6 | 9 |
P value = 0.818 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 66 | 1 | 2 | 1 |
subtype1 | 11 | 0 | 0 | 0 |
subtype2 | 17 | 1 | 1 | 1 |
subtype3 | 14 | 0 | 0 | 0 |
subtype4 | 11 | 0 | 0 | 0 |
subtype5 | 13 | 0 | 1 | 0 |
P value = 0.424 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 45 | 1 | 1 | 7 | 2 | 4 | 1 | 8 | 2 |
subtype1 | 6 | 0 | 1 | 2 | 0 | 0 | 0 | 2 | 0 |
subtype2 | 16 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 0 |
subtype3 | 10 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 1 |
subtype4 | 7 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | 0 |
subtype5 | 6 | 0 | 0 | 2 | 1 | 2 | 0 | 2 | 1 |
P value = 0.512 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 11 | 6 | 6 | 8 | 5 | 4 | 2 | 2 | 1 | 6 | 10 | 3 |
subtype1 | 0 | 2 | 0 | 2 | 1 | 1 | 0 | 0 | 0 | 1 | 1 | 3 | 0 |
subtype2 | 1 | 4 | 1 | 1 | 4 | 3 | 1 | 0 | 1 | 0 | 0 | 0 | 3 |
subtype3 | 0 | 2 | 2 | 1 | 2 | 1 | 0 | 1 | 1 | 0 | 1 | 1 | 0 |
subtype4 | 0 | 2 | 1 | 0 | 1 | 0 | 2 | 1 | 0 | 0 | 2 | 3 | 0 |
subtype5 | 0 | 1 | 2 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 22 | 34 | 12 |
P value = 0.0406 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 40 | 22 | 1.1 - 98.8 (13.5) |
subtype1 | 8 | 1 | 5.1 - 98.8 (10.8) |
subtype2 | 8 | 4 | 4.2 - 42.8 (19.3) |
subtype3 | 15 | 13 | 1.1 - 78.4 (13.0) |
subtype4 | 9 | 4 | 8.4 - 84.7 (16.5) |
P value = 0.856 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 56.5 (15.9) |
subtype1 | 12 | 56.9 (14.7) |
subtype2 | 22 | 58.1 (14.3) |
subtype3 | 34 | 56.6 (17.4) |
subtype4 | 12 | 53.1 (17.0) |
P value = 0.0741 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 29 | 51 |
subtype1 | 8 | 4 |
subtype2 | 5 | 17 |
subtype3 | 13 | 21 |
subtype4 | 3 | 9 |
P value = 0.489 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 66 | 1 | 2 | 1 |
subtype1 | 12 | 0 | 0 | 0 |
subtype2 | 13 | 1 | 1 | 1 |
subtype3 | 30 | 0 | 1 | 0 |
subtype4 | 11 | 0 | 0 | 0 |
P value = 0.177 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 45 | 1 | 1 | 7 | 2 | 4 | 1 | 8 | 2 |
subtype1 | 8 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 1 |
subtype2 | 13 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 0 |
subtype3 | 19 | 0 | 0 | 3 | 2 | 2 | 0 | 4 | 1 |
subtype4 | 5 | 0 | 1 | 3 | 0 | 0 | 0 | 2 | 0 |
P value = 0.0129 (Chi-square test), Q value = 0.61
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 11 | 6 | 6 | 8 | 5 | 4 | 2 | 2 | 1 | 6 | 10 | 3 |
subtype1 | 0 | 2 | 2 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 0 |
subtype2 | 1 | 5 | 0 | 0 | 0 | 4 | 1 | 1 | 0 | 0 | 1 | 0 | 3 |
subtype3 | 0 | 2 | 4 | 3 | 7 | 0 | 3 | 0 | 1 | 0 | 2 | 6 | 0 |
subtype4 | 0 | 2 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 1 | 2 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 42 | 27 | 43 |
P value = 0.109 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 59 | 32 | 1.0 - 98.8 (13.0) |
subtype1 | 18 | 11 | 4.2 - 51.1 (13.2) |
subtype2 | 15 | 6 | 1.1 - 98.8 (23.9) |
subtype3 | 26 | 15 | 1.0 - 72.2 (10.9) |
P value = 0.387 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 112 | 55.4 (16.4) |
subtype1 | 42 | 52.7 (17.5) |
subtype2 | 27 | 57.2 (14.1) |
subtype3 | 43 | 57.0 (16.7) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 77 |
subtype1 | 13 | 29 |
subtype2 | 8 | 19 |
subtype3 | 14 | 29 |
P value = 0.702 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 98 | 1 | 2 | 1 |
subtype1 | 37 | 1 | 1 | 1 |
subtype2 | 24 | 0 | 0 | 0 |
subtype3 | 37 | 0 | 1 | 0 |
P value = 0.432 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 61 | 1 | 3 | 10 | 1 | 3 | 8 | 1 | 13 | 2 |
subtype1 | 26 | 0 | 1 | 3 | 0 | 0 | 2 | 1 | 5 | 2 |
subtype2 | 15 | 1 | 0 | 2 | 0 | 0 | 3 | 0 | 3 | 0 |
subtype3 | 20 | 0 | 2 | 5 | 1 | 3 | 3 | 0 | 5 | 0 |
P value = 0.113 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 13 | 5 | 5 | 2 | 4 | 3 | 10 | 18 | 3 |
subtype1 | 1 | 7 | 1 | 4 | 7 | 3 | 2 | 1 | 1 | 0 | 2 | 6 | 3 |
subtype2 | 0 | 6 | 0 | 3 | 3 | 2 | 0 | 0 | 1 | 0 | 4 | 4 | 0 |
subtype3 | 0 | 2 | 6 | 4 | 3 | 0 | 3 | 1 | 2 | 3 | 4 | 8 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 18 | 29 | 34 | 31 |
P value = 0.636 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 59 | 32 | 1.0 - 98.8 (13.0) |
subtype1 | 9 | 5 | 2.9 - 72.2 (11.1) |
subtype2 | 16 | 7 | 1.1 - 78.4 (18.0) |
subtype3 | 14 | 9 | 6.5 - 84.7 (14.5) |
subtype4 | 20 | 11 | 1.0 - 98.8 (10.5) |
P value = 0.0724 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 112 | 55.4 (16.4) |
subtype1 | 18 | 50.9 (15.8) |
subtype2 | 29 | 57.5 (14.4) |
subtype3 | 34 | 51.4 (17.0) |
subtype4 | 31 | 60.6 (16.8) |
P value = 0.671 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 77 |
subtype1 | 4 | 14 |
subtype2 | 8 | 21 |
subtype3 | 13 | 21 |
subtype4 | 10 | 21 |
P value = 0.558 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 98 | 1 | 2 | 1 |
subtype1 | 17 | 0 | 1 | 0 |
subtype2 | 27 | 0 | 0 | 0 |
subtype3 | 29 | 0 | 1 | 1 |
subtype4 | 25 | 1 | 0 | 0 |
P value = 0.531 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 61 | 1 | 3 | 10 | 1 | 3 | 8 | 1 | 13 | 2 |
subtype1 | 10 | 0 | 2 | 2 | 0 | 1 | 2 | 0 | 1 | 0 |
subtype2 | 18 | 0 | 0 | 3 | 0 | 0 | 3 | 0 | 3 | 0 |
subtype3 | 19 | 1 | 0 | 3 | 0 | 0 | 1 | 1 | 4 | 2 |
subtype4 | 14 | 0 | 1 | 2 | 1 | 2 | 2 | 0 | 5 | 0 |
P value = 0.102 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 13 | 5 | 5 | 2 | 4 | 3 | 10 | 18 | 3 |
subtype1 | 0 | 1 | 2 | 2 | 3 | 0 | 1 | 0 | 1 | 1 | 5 | 0 | 0 |
subtype2 | 0 | 6 | 1 | 3 | 4 | 2 | 0 | 1 | 0 | 0 | 4 | 5 | 0 |
subtype3 | 1 | 6 | 0 | 3 | 6 | 2 | 1 | 0 | 2 | 0 | 0 | 6 | 2 |
subtype4 | 0 | 2 | 4 | 3 | 0 | 1 | 3 | 1 | 1 | 2 | 1 | 7 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 42 | 23 | 45 |
P value = 0.304 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 57 | 32 | 1.0 - 98.8 (13.0) |
subtype1 | 21 | 13 | 1.1 - 48.8 (8.9) |
subtype2 | 12 | 6 | 11.1 - 84.7 (16.2) |
subtype3 | 24 | 13 | 1.0 - 98.8 (12.3) |
P value = 0.0367 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 55.5 (16.2) |
subtype1 | 42 | 58.7 (16.5) |
subtype2 | 23 | 58.8 (16.4) |
subtype3 | 45 | 50.7 (15.0) |
P value = 0.496 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 76 |
subtype1 | 15 | 27 |
subtype2 | 8 | 15 |
subtype3 | 11 | 34 |
P value = 0.29 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 96 | 1 | 2 | 1 |
subtype1 | 39 | 0 | 1 | 0 |
subtype2 | 18 | 0 | 1 | 1 |
subtype3 | 39 | 1 | 0 | 0 |
P value = 0.854 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 60 | 1 | 3 | 10 | 1 | 3 | 8 | 1 | 12 | 2 |
subtype1 | 24 | 0 | 1 | 4 | 0 | 1 | 5 | 0 | 5 | 0 |
subtype2 | 11 | 0 | 1 | 3 | 0 | 1 | 1 | 1 | 2 | 1 |
subtype3 | 25 | 1 | 1 | 3 | 1 | 1 | 2 | 0 | 5 | 1 |
P value = 0.00574 (Chi-square test), Q value = 0.28
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 12 | 5 | 5 | 2 | 4 | 3 | 10 | 17 | 3 |
subtype1 | 0 | 4 | 5 | 4 | 7 | 1 | 3 | 0 | 0 | 0 | 6 | 8 | 0 |
subtype2 | 1 | 2 | 1 | 0 | 3 | 1 | 0 | 2 | 1 | 1 | 4 | 1 | 2 |
subtype3 | 0 | 9 | 1 | 7 | 2 | 3 | 2 | 0 | 3 | 2 | 0 | 8 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 11 | 25 | 74 |
P value = 0.275 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 57 | 32 | 1.0 - 98.8 (13.0) |
subtype1 | 5 | 2 | 11.3 - 23.9 (14.8) |
subtype2 | 13 | 7 | 6.5 - 84.7 (21.1) |
subtype3 | 39 | 23 | 1.0 - 98.8 (11.1) |
P value = 0.305 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 55.5 (16.2) |
subtype1 | 11 | 62.3 (15.1) |
subtype2 | 25 | 53.4 (13.4) |
subtype3 | 74 | 55.1 (17.1) |
P value = 0.158 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 76 |
subtype1 | 4 | 7 |
subtype2 | 4 | 21 |
subtype3 | 26 | 48 |
P value = 0.526 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 96 | 1 | 2 | 1 |
subtype1 | 11 | 0 | 0 | 0 |
subtype2 | 20 | 0 | 1 | 1 |
subtype3 | 65 | 1 | 1 | 0 |
P value = 0.296 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 60 | 1 | 3 | 10 | 1 | 3 | 8 | 1 | 12 | 2 |
subtype1 | 5 | 0 | 1 | 2 | 0 | 1 | 1 | 0 | 0 | 1 |
subtype2 | 13 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 5 | 1 |
subtype3 | 42 | 1 | 2 | 6 | 1 | 2 | 7 | 0 | 7 | 0 |
P value = 0.0351 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 15 | 7 | 11 | 12 | 5 | 5 | 2 | 4 | 3 | 10 | 17 | 3 |
subtype1 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 1 | 0 | 1 | 4 | 0 | 0 |
subtype2 | 1 | 7 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | 5 | 2 |
subtype3 | 0 | 8 | 5 | 10 | 9 | 3 | 4 | 1 | 3 | 2 | 6 | 12 | 1 |
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Cluster data file = SKCM-Regional_LN.mergedcluster.txt
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Clinical data file = SKCM-Regional_LN.clin.merged.picked.txt
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Number of patients = 116
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Number of clustering approaches = 8
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Number of selected clinical features = 7
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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
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.