(Regional_Metastatic 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 8 clinical features across 152 patients, 3 significant findings 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.
-
3 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 3 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 correlate to 'PRIMARY.SITE.OF.DISEASE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'PRIMARY.SITE.OF.DISEASE'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE'.
-
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 |
PRIMARY SITE OF DISEASE |
GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.618 (1.00) |
0.124 (1.00) |
0.338 (1.00) |
0.575 (1.00) |
0.535 (1.00) |
0.527 (1.00) |
0.395 (1.00) |
|
METHLYATION CNMF |
0.449 (1.00) |
0.12 (1.00) |
0.0552 (1.00) |
0.081 (1.00) |
0.699 (1.00) |
0.418 (1.00) |
0.403 (1.00) |
|
RPPA CNMF subtypes |
0.914 (1.00) |
0.661 (1.00) |
0.0295 (1.00) |
0.766 (1.00) |
0.513 (1.00) |
0.165 (1.00) |
0.036 (1.00) |
|
RPPA cHierClus subtypes |
0.13 (1.00) |
0.897 (1.00) |
0.0609 (1.00) |
0.0632 (1.00) |
0.427 (1.00) |
0.0246 (1.00) |
0.00868 (0.451) |
|
RNAseq CNMF subtypes |
0.124 (1.00) |
0.00657 (0.348) |
1.6e-06 (8.98e-05) |
0.703 (1.00) |
0.782 (1.00) |
0.625 (1.00) |
0.0265 (1.00) |
|
RNAseq cHierClus subtypes |
0.0433 (1.00) |
0.0108 (0.552) |
0.000359 (0.0198) |
0.551 (1.00) |
0.532 (1.00) |
0.86 (1.00) |
0.052 (1.00) |
|
MIRSEQ CNMF |
0.425 (1.00) |
0.0885 (1.00) |
0.00304 (0.164) |
0.585 (1.00) |
0.263 (1.00) |
0.809 (1.00) |
0.0444 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.766 (1.00) |
0.964 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.274 (1.00) |
0.548 (1.00) |
0.296 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 26 | 41 | 56 |
P value = 0.618 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 145 | 69 | 2.6 - 346.0 (47.5) |
subtype1 | 24 | 11 | 2.6 - 194.8 (40.0) |
subtype2 | 26 | 12 | 3.2 - 346.0 (61.1) |
subtype3 | 40 | 23 | 2.7 - 248.6 (48.1) |
subtype4 | 55 | 23 | 4.2 - 314.5 (43.2) |
P value = 0.124 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 147 | 56.0 (16.0) |
subtype1 | 24 | 61.0 (14.9) |
subtype2 | 26 | 51.2 (15.6) |
subtype3 | 41 | 58.0 (17.2) |
subtype4 | 56 | 54.7 (15.2) |
P value = 0.338 (Fisher's exact test), Q value = 1
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 35 | 112 |
subtype1 | 7 | 17 |
subtype2 | 8 | 18 |
subtype3 | 11 | 30 |
subtype4 | 9 | 47 |
P value = 0.575 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 52 | 95 |
subtype1 | 10 | 14 |
subtype2 | 10 | 16 |
subtype3 | 16 | 25 |
subtype4 | 16 | 40 |
P value = 0.535 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 128 | 1 | 2 | 2 | 1 |
subtype1 | 21 | 0 | 0 | 0 | 1 |
subtype2 | 22 | 0 | 0 | 1 | 0 |
subtype3 | 36 | 1 | 1 | 0 | 0 |
subtype4 | 49 | 0 | 1 | 1 | 0 |
P value = 0.527 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 2 | 6 | 12 | 1 | 4 | 11 | 4 | 16 | 2 |
subtype1 | 11 | 0 | 2 | 1 | 0 | 0 | 1 | 2 | 4 | 1 |
subtype2 | 12 | 0 | 1 | 3 | 0 | 2 | 1 | 0 | 3 | 1 |
subtype3 | 23 | 0 | 2 | 5 | 0 | 1 | 4 | 2 | 2 | 0 |
subtype4 | 31 | 2 | 1 | 3 | 1 | 1 | 5 | 0 | 7 | 0 |
P value = 0.395 (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 | 16 | 8 | 13 | 17 | 7 | 8 | 4 | 8 | 5 | 16 | 21 | 4 |
subtype1 | 0 | 2 | 2 | 2 | 2 | 2 | 1 | 0 | 1 | 2 | 1 | 5 | 1 |
subtype2 | 1 | 1 | 2 | 2 | 4 | 0 | 0 | 2 | 0 | 1 | 5 | 3 | 0 |
subtype3 | 0 | 2 | 1 | 4 | 7 | 1 | 4 | 2 | 3 | 1 | 5 | 4 | 2 |
subtype4 | 0 | 11 | 3 | 5 | 4 | 4 | 3 | 0 | 4 | 1 | 5 | 9 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 57 | 52 |
P value = 0.449 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 150 | 71 | 0.9 - 346.0 (47.5) |
subtype1 | 43 | 23 | 7.8 - 204.6 (43.4) |
subtype2 | 55 | 26 | 2.7 - 346.0 (46.8) |
subtype3 | 52 | 22 | 0.9 - 248.6 (49.2) |
P value = 0.12 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 152 | 55.9 (15.9) |
subtype1 | 43 | 55.5 (16.2) |
subtype2 | 57 | 53.1 (13.9) |
subtype3 | 52 | 59.4 (17.3) |
P value = 0.0552 (Fisher's exact test), Q value = 1
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 36 | 116 |
subtype1 | 16 | 27 |
subtype2 | 10 | 47 |
subtype3 | 10 | 42 |
P value = 0.081 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 55 | 97 |
subtype1 | 14 | 29 |
subtype2 | 16 | 41 |
subtype3 | 25 | 27 |
P value = 0.699 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 133 | 1 | 2 | 2 | 1 |
subtype1 | 39 | 0 | 1 | 0 | 0 |
subtype2 | 50 | 0 | 1 | 1 | 1 |
subtype3 | 44 | 1 | 0 | 1 | 0 |
P value = 0.418 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 78 | 2 | 7 | 12 | 1 | 4 | 12 | 4 | 18 | 2 |
subtype1 | 23 | 0 | 4 | 4 | 1 | 1 | 4 | 2 | 2 | 0 |
subtype2 | 28 | 2 | 1 | 7 | 0 | 1 | 5 | 1 | 7 | 1 |
subtype3 | 27 | 0 | 2 | 1 | 0 | 2 | 3 | 1 | 9 | 1 |
P value = 0.403 (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 | 16 | 8 | 14 | 17 | 7 | 8 | 4 | 9 | 5 | 17 | 23 | 4 |
subtype1 | 1 | 2 | 0 | 4 | 8 | 2 | 3 | 2 | 5 | 2 | 5 | 6 | 1 |
subtype2 | 0 | 10 | 3 | 5 | 5 | 3 | 1 | 0 | 4 | 1 | 7 | 8 | 2 |
subtype3 | 0 | 4 | 5 | 5 | 4 | 2 | 4 | 2 | 0 | 2 | 5 | 9 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 22 | 36 | 37 |
P value = 0.914 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 94 | 47 | 2.6 - 346.0 (47.7) |
subtype1 | 22 | 12 | 12.6 - 346.0 (50.5) |
subtype2 | 36 | 17 | 4.2 - 204.6 (51.2) |
subtype3 | 36 | 18 | 2.6 - 216.9 (43.3) |
P value = 0.661 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 95 | 56.9 (15.9) |
subtype1 | 22 | 55.3 (15.4) |
subtype2 | 36 | 56.0 (15.9) |
subtype3 | 37 | 58.8 (16.5) |
P value = 0.0295 (Fisher's exact test), Q value = 1
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 15 | 80 |
subtype1 | 7 | 15 |
subtype2 | 2 | 34 |
subtype3 | 6 | 31 |
P value = 0.766 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 60 |
subtype1 | 9 | 13 |
subtype2 | 14 | 22 |
subtype3 | 12 | 25 |
P value = 0.513 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 78 | 1 | 2 | 1 |
subtype1 | 21 | 0 | 0 | 0 |
subtype2 | 23 | 1 | 1 | 1 |
subtype3 | 34 | 0 | 1 | 0 |
P value = 0.165 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 48 | 2 | 3 | 9 | 2 | 5 | 3 | 9 | 2 |
subtype1 | 9 | 0 | 3 | 3 | 0 | 2 | 0 | 3 | 1 |
subtype2 | 21 | 0 | 0 | 2 | 0 | 1 | 1 | 2 | 0 |
subtype3 | 18 | 2 | 0 | 4 | 2 | 2 | 2 | 4 | 1 |
P value = 0.036 (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 | 7 | 7 | 9 | 5 | 4 | 2 | 5 | 2 | 9 | 11 | 3 |
subtype1 | 0 | 3 | 1 | 3 | 1 | 1 | 0 | 0 | 1 | 2 | 3 | 5 | 0 |
subtype2 | 1 | 7 | 2 | 1 | 3 | 3 | 1 | 2 | 1 | 0 | 2 | 0 | 3 |
subtype3 | 0 | 1 | 4 | 3 | 5 | 1 | 3 | 0 | 3 | 0 | 4 | 6 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 16 | 26 | 34 | 19 |
P value = 0.13 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 94 | 47 | 2.6 - 346.0 (47.7) |
subtype1 | 16 | 10 | 13.9 - 117.2 (47.3) |
subtype2 | 26 | 14 | 4.2 - 204.6 (36.1) |
subtype3 | 33 | 17 | 2.6 - 216.9 (55.6) |
subtype4 | 19 | 6 | 2.7 - 346.0 (54.7) |
P value = 0.897 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 95 | 56.9 (15.9) |
subtype1 | 16 | 56.3 (16.6) |
subtype2 | 26 | 56.1 (15.0) |
subtype3 | 34 | 56.5 (16.3) |
subtype4 | 19 | 59.5 (17.0) |
P value = 0.0609 (Fisher's exact test), Q value = 1
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 15 | 80 |
subtype1 | 5 | 11 |
subtype2 | 4 | 22 |
subtype3 | 6 | 28 |
subtype4 | 0 | 19 |
P value = 0.0632 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 60 |
subtype1 | 4 | 12 |
subtype2 | 7 | 19 |
subtype3 | 12 | 22 |
subtype4 | 12 | 7 |
P value = 0.427 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 78 | 1 | 2 | 1 |
subtype1 | 15 | 0 | 0 | 0 |
subtype2 | 15 | 1 | 1 | 1 |
subtype3 | 29 | 0 | 1 | 0 |
subtype4 | 19 | 0 | 0 | 0 |
P value = 0.0246 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 48 | 2 | 3 | 9 | 2 | 5 | 3 | 9 | 2 |
subtype1 | 6 | 0 | 3 | 3 | 0 | 1 | 0 | 2 | 0 |
subtype2 | 14 | 0 | 0 | 1 | 0 | 0 | 1 | 3 | 0 |
subtype3 | 17 | 1 | 0 | 4 | 0 | 2 | 2 | 4 | 0 |
subtype4 | 11 | 1 | 0 | 1 | 2 | 2 | 0 | 0 | 2 |
P value = 0.00868 (Chi-square test), Q value = 0.45
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 | 7 | 7 | 9 | 5 | 4 | 2 | 5 | 2 | 9 | 11 | 3 |
subtype1 | 0 | 2 | 1 | 2 | 0 | 1 | 0 | 0 | 1 | 2 | 3 | 3 | 0 |
subtype2 | 1 | 5 | 0 | 1 | 0 | 4 | 1 | 1 | 0 | 0 | 1 | 1 | 3 |
subtype3 | 0 | 1 | 4 | 3 | 6 | 0 | 3 | 0 | 3 | 0 | 2 | 6 | 0 |
subtype4 | 0 | 3 | 2 | 1 | 3 | 0 | 0 | 1 | 1 | 0 | 3 | 1 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 56 | 38 | 51 |
P value = 0.124 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 143 | 69 | 2.6 - 346.0 (47.5) |
subtype1 | 56 | 31 | 6.4 - 346.0 (61.1) |
subtype2 | 37 | 13 | 4.2 - 203.0 (49.5) |
subtype3 | 50 | 25 | 2.6 - 216.9 (39.6) |
P value = 0.00657 (ANOVA), Q value = 0.35
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 145 | 56.0 (16.1) |
subtype1 | 56 | 51.4 (15.9) |
subtype2 | 38 | 55.9 (15.3) |
subtype3 | 51 | 61.1 (15.6) |
P value = 1.6e-06 (Fisher's exact test), Q value = 9e-05
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 33 | 112 |
subtype1 | 23 | 33 |
subtype2 | 0 | 38 |
subtype3 | 10 | 41 |
P value = 0.703 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 51 | 94 |
subtype1 | 22 | 34 |
subtype2 | 12 | 26 |
subtype3 | 17 | 34 |
P value = 0.782 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 126 | 1 | 2 | 2 | 1 |
subtype1 | 47 | 1 | 1 | 1 | 1 |
subtype2 | 35 | 0 | 0 | 0 | 0 |
subtype3 | 44 | 0 | 1 | 1 | 0 |
P value = 0.625 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 2 | 5 | 12 | 1 | 4 | 10 | 4 | 16 | 2 |
subtype1 | 28 | 1 | 2 | 4 | 0 | 1 | 3 | 3 | 7 | 2 |
subtype2 | 25 | 1 | 1 | 2 | 0 | 0 | 3 | 0 | 3 | 0 |
subtype3 | 24 | 0 | 2 | 6 | 1 | 3 | 4 | 1 | 6 | 0 |
P value = 0.0265 (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 | 16 | 8 | 13 | 17 | 7 | 8 | 4 | 8 | 4 | 15 | 21 | 4 |
subtype1 | 1 | 7 | 0 | 5 | 9 | 2 | 3 | 0 | 5 | 1 | 4 | 8 | 4 |
subtype2 | 0 | 7 | 3 | 3 | 6 | 4 | 0 | 1 | 1 | 0 | 5 | 4 | 0 |
subtype3 | 0 | 2 | 5 | 5 | 2 | 1 | 5 | 3 | 2 | 3 | 6 | 9 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 48 | 64 | 33 |
P value = 0.0433 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 143 | 69 | 2.6 - 346.0 (47.5) |
subtype1 | 48 | 28 | 7.8 - 216.9 (63.5) |
subtype2 | 63 | 22 | 2.7 - 346.0 (44.0) |
subtype3 | 32 | 19 | 2.6 - 314.5 (39.6) |
P value = 0.0108 (ANOVA), Q value = 0.55
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 145 | 56.0 (16.1) |
subtype1 | 48 | 50.9 (15.5) |
subtype2 | 64 | 56.9 (15.4) |
subtype3 | 33 | 61.5 (16.5) |
P value = 0.000359 (Fisher's exact test), Q value = 0.02
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 33 | 112 |
subtype1 | 16 | 32 |
subtype2 | 5 | 59 |
subtype3 | 12 | 21 |
P value = 0.551 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 51 | 94 |
subtype1 | 17 | 31 |
subtype2 | 20 | 44 |
subtype3 | 14 | 19 |
P value = 0.532 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 126 | 1 | 2 | 2 | 1 |
subtype1 | 39 | 0 | 1 | 1 | 1 |
subtype2 | 59 | 0 | 1 | 1 | 0 |
subtype3 | 28 | 1 | 0 | 0 | 0 |
P value = 0.86 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 77 | 2 | 5 | 12 | 1 | 4 | 10 | 4 | 16 | 2 |
subtype1 | 27 | 0 | 1 | 4 | 0 | 1 | 2 | 2 | 5 | 0 |
subtype2 | 35 | 1 | 3 | 6 | 1 | 2 | 4 | 0 | 7 | 2 |
subtype3 | 15 | 1 | 1 | 2 | 0 | 1 | 4 | 2 | 4 | 0 |
P value = 0.052 (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 | 16 | 8 | 13 | 17 | 7 | 8 | 4 | 8 | 4 | 15 | 21 | 4 |
subtype1 | 1 | 7 | 0 | 6 | 8 | 3 | 1 | 0 | 3 | 1 | 2 | 7 | 3 |
subtype2 | 0 | 8 | 7 | 5 | 7 | 3 | 2 | 1 | 2 | 2 | 9 | 8 | 0 |
subtype3 | 0 | 1 | 1 | 2 | 2 | 1 | 5 | 3 | 3 | 1 | 4 | 6 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 56 | 29 | 59 |
P value = 0.425 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 142 | 69 | 2.6 - 346.0 (47.5) |
subtype1 | 56 | 27 | 2.6 - 216.9 (40.6) |
subtype2 | 28 | 11 | 6.4 - 248.6 (47.4) |
subtype3 | 58 | 31 | 6.4 - 346.0 (55.7) |
P value = 0.0885 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 144 | 55.9 (15.8) |
subtype1 | 56 | 58.9 (16.0) |
subtype2 | 29 | 57.0 (16.5) |
subtype3 | 59 | 52.5 (14.8) |
P value = 0.00304 (Fisher's exact test), Q value = 0.16
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 34 | 110 |
subtype1 | 6 | 50 |
subtype2 | 6 | 23 |
subtype3 | 22 | 37 |
P value = 0.585 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 50 | 94 |
subtype1 | 20 | 36 |
subtype2 | 12 | 17 |
subtype3 | 18 | 41 |
P value = 0.263 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 125 | 1 | 2 | 2 | 1 |
subtype1 | 50 | 0 | 1 | 1 | 0 |
subtype2 | 21 | 0 | 1 | 1 | 1 |
subtype3 | 54 | 1 | 0 | 0 | 0 |
P value = 0.809 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 2 | 6 | 12 | 1 | 4 | 11 | 4 | 15 | 2 |
subtype1 | 31 | 0 | 2 | 5 | 0 | 2 | 5 | 1 | 6 | 0 |
subtype2 | 12 | 0 | 1 | 3 | 0 | 2 | 1 | 1 | 4 | 1 |
subtype3 | 32 | 2 | 3 | 4 | 1 | 0 | 5 | 2 | 5 | 1 |
P value = 0.0444 (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 | 16 | 8 | 13 | 16 | 6 | 8 | 4 | 8 | 5 | 16 | 20 | 4 |
subtype1 | 0 | 4 | 5 | 4 | 9 | 3 | 5 | 0 | 0 | 2 | 7 | 9 | 1 |
subtype2 | 1 | 2 | 1 | 0 | 4 | 1 | 0 | 2 | 1 | 1 | 5 | 3 | 2 |
subtype3 | 0 | 10 | 2 | 9 | 3 | 2 | 3 | 2 | 7 | 2 | 4 | 8 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 18 | 94 |
P value = 0.766 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 142 | 69 | 2.6 - 346.0 (47.5) |
subtype1 | 32 | 18 | 10.1 - 346.0 (61.3) |
subtype2 | 17 | 5 | 6.4 - 203.0 (28.8) |
subtype3 | 93 | 46 | 2.6 - 314.5 (47.3) |
P value = 0.964 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 144 | 55.9 (15.8) |
subtype1 | 32 | 55.3 (12.6) |
subtype2 | 18 | 56.6 (16.6) |
subtype3 | 94 | 56.0 (16.7) |
P value = 0.373 (Fisher's exact test), Q value = 1
nPatients | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|
ALL | 34 | 110 |
subtype1 | 10 | 22 |
subtype2 | 5 | 13 |
subtype3 | 19 | 75 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 50 | 94 |
subtype1 | 11 | 21 |
subtype2 | 6 | 12 |
subtype3 | 33 | 61 |
P value = 0.274 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 125 | 1 | 2 | 2 | 1 |
subtype1 | 28 | 0 | 0 | 0 | 1 |
subtype2 | 14 | 0 | 1 | 1 | 0 |
subtype3 | 83 | 1 | 1 | 1 | 0 |
P value = 0.548 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 2 | 6 | 12 | 1 | 4 | 11 | 4 | 15 | 2 |
subtype1 | 16 | 1 | 1 | 3 | 0 | 0 | 1 | 1 | 5 | 1 |
subtype2 | 6 | 0 | 1 | 2 | 0 | 2 | 2 | 0 | 2 | 1 |
subtype3 | 53 | 1 | 4 | 7 | 1 | 2 | 8 | 3 | 8 | 0 |
P value = 0.296 (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 | 16 | 8 | 13 | 16 | 6 | 8 | 4 | 8 | 5 | 16 | 20 | 4 |
subtype1 | 0 | 7 | 1 | 2 | 2 | 1 | 2 | 1 | 3 | 1 | 1 | 6 | 1 |
subtype2 | 0 | 0 | 1 | 0 | 3 | 1 | 0 | 1 | 0 | 1 | 6 | 1 | 1 |
subtype3 | 1 | 9 | 6 | 11 | 11 | 4 | 6 | 2 | 5 | 3 | 9 | 13 | 2 |
-
Cluster data file = SKCM-Regional_Metastatic.mergedcluster.txt
-
Clinical data file = SKCM-Regional_Metastatic.clin.merged.picked.txt
-
Number of patients = 152
-
Number of clustering approaches = 8
-
Number of selected clinical features = 8
-
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.