(NRAS_Hotspot_Mutants 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 45 patients, 4 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 2 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 5 subtypes that correlate to 'Time to Death'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'PRIMARY.SITE.OF.DISEASE'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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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 |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Chi-square test | Fisher's exact test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.37 (1.00) |
0.656 (1.00) |
0.913 (1.00) |
0.369 (1.00) |
0.714 (1.00) |
0.435 (1.00) |
|
METHLYATION CNMF |
0.409 (1.00) |
0.0278 (1.00) |
0.16 (1.00) |
0.287 (1.00) |
0.693 (1.00) |
0.839 (1.00) |
|
RPPA CNMF subtypes |
0.0113 (0.499) |
0.149 (1.00) |
0.795 (1.00) |
0.466 (1.00) |
0.915 (1.00) |
0.673 (1.00) |
|
RPPA cHierClus subtypes |
0.0044 (0.198) |
0.341 (1.00) |
0.269 (1.00) |
0.426 (1.00) |
0.494 (1.00) |
0.19 (1.00) |
|
RNAseq CNMF subtypes |
0.00161 (0.0755) |
0.633 (1.00) |
0.0337 (1.00) |
0.0833 (1.00) |
0.881 (1.00) |
0.629 (1.00) |
|
RNAseq cHierClus subtypes |
0.00176 (0.0809) |
0.83 (1.00) |
0.00122 (0.0587) |
0.157 (1.00) |
0.905 (1.00) |
0.547 (1.00) |
|
MIRSEQ CNMF |
0.647 (1.00) |
0.294 (1.00) |
0.423 (1.00) |
0.579 (1.00) |
0.144 (1.00) |
0.226 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.495 (1.00) |
0.242 (1.00) |
0.58 (1.00) |
1 (1.00) |
0.151 (1.00) |
0.121 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 12 | 8 | 12 | 13 |
P value = 0.37 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 9 | 6 | 2.4 - 48.8 (10.0) |
subtype2 | 3 | 3 | 3.5 - 28.1 (11.6) |
subtype3 | 5 | 1 | 8.1 - 42.8 (23.9) |
subtype4 | 5 | 3 | 1.1 - 39.2 (8.8) |
P value = 0.656 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 12 | 61.8 (20.7) |
subtype2 | 8 | 53.1 (14.8) |
subtype3 | 12 | 56.2 (11.3) |
subtype4 | 13 | 58.4 (14.2) |
P value = 0.913 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 3 | 2 | 7 |
subtype2 | 1 | 2 | 5 |
subtype3 | 1 | 2 | 9 |
subtype4 | 3 | 3 | 7 |
P value = 0.369 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 6 | 6 |
subtype2 | 4 | 4 |
subtype3 | 3 | 9 |
subtype4 | 3 | 10 |
P value = 0.714 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 5 | 2 | 1 | 1 | 1 | 2 |
subtype2 | 6 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 8 | 1 | 1 | 0 | 0 | 0 |
subtype4 | 8 | 0 | 2 | 0 | 1 | 2 |
P value = 0.435 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 1 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 3 | 3 | 0 |
subtype2 | 0 | 1 | 1 | 1 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 0 | 1 | 0 | 3 | 1 | 1 | 2 | 0 | 0 | 0 | 2 | 0 | 0 |
subtype4 | 0 | 1 | 3 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 15 | 14 | 16 |
P value = 0.409 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 6 | 5 | 3.5 - 16.5 (9.3) |
subtype2 | 6 | 3 | 2.4 - 42.8 (16.8) |
subtype3 | 10 | 5 | 1.1 - 48.8 (10.8) |
P value = 0.0278 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 15 | 54.6 (15.3) |
subtype2 | 14 | 52.0 (15.2) |
subtype3 | 16 | 65.8 (12.9) |
P value = 0.16 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 4 | 4 | 7 |
subtype2 | 4 | 2 | 8 |
subtype3 | 0 | 3 | 13 |
P value = 0.287 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 5 | 10 |
subtype2 | 3 | 11 |
subtype3 | 8 | 8 |
P value = 0.693 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 8 | 2 | 1 | 0 | 1 | 1 |
subtype2 | 8 | 1 | 2 | 1 | 0 | 1 |
subtype3 | 11 | 0 | 1 | 0 | 1 | 3 |
P value = 0.839 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 0 | 0 | 1 | 3 | 1 | 1 | 1 | 1 | 0 | 1 | 2 | 2 | 0 |
subtype2 | 1 | 1 | 0 | 2 | 2 | 1 | 1 | 0 | 1 | 0 | 2 | 1 | 1 |
subtype3 | 0 | 2 | 3 | 1 | 1 | 1 | 2 | 1 | 0 | 0 | 2 | 3 | 0 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 16 | 14 |
P value = 0.0113 (logrank test), Q value = 0.5
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 15 | 10 | 1.1 - 48.8 (11.6) |
subtype1 | 7 | 4 | 3.5 - 48.8 (23.9) |
subtype2 | 8 | 6 | 1.1 - 15.4 (8.6) |
P value = 0.149 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 57.5 (16.7) |
subtype1 | 16 | 53.3 (14.4) |
subtype2 | 14 | 62.4 (18.3) |
P value = 0.795 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 5 | 2 | 23 |
subtype1 | 2 | 1 | 13 |
subtype2 | 3 | 1 | 10 |
P value = 0.466 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 11 | 19 |
subtype1 | 7 | 9 |
subtype2 | 4 | 10 |
P value = 0.915 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|
ALL | 16 | 2 | 4 | 1 | 4 |
subtype1 | 8 | 1 | 2 | 1 | 2 |
subtype2 | 8 | 1 | 2 | 0 | 2 |
P value = 0.673 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 3 | 3 | 3 | 3 | 2 | 1 | 1 | 1 | 3 | 5 | 1 |
subtype1 | 0 | 2 | 2 | 2 | 1 | 1 | 0 | 1 | 1 | 2 | 1 | 1 |
subtype2 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | 0 | 1 | 4 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 3 | 4 | 1 | 5 | 7 | 10 |
P value = 0.0044 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 15 | 10 | 1.1 - 48.8 (11.6) |
subtype1 | 1 | 0 | 10.0 - 10.0 (10.0) |
subtype2 | 2 | 2 | 2.4 - 8.4 (5.4) |
subtype4 | 5 | 4 | 3.5 - 28.1 (16.2) |
subtype5 | 3 | 0 | 23.9 - 48.8 (42.8) |
subtype6 | 4 | 4 | 1.1 - 15.4 (7.9) |
P value = 0.341 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 29 | 58.4 (16.3) |
subtype1 | 3 | 57.0 (20.0) |
subtype2 | 4 | 71.5 (16.4) |
subtype4 | 5 | 48.8 (17.9) |
subtype5 | 7 | 60.9 (10.9) |
subtype6 | 10 | 56.7 (16.9) |
P value = 0.269 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 4 | 2 | 23 |
subtype1 | 0 | 0 | 3 |
subtype2 | 1 | 1 | 2 |
subtype4 | 0 | 1 | 4 |
subtype5 | 0 | 0 | 7 |
subtype6 | 3 | 0 | 7 |
P value = 0.426 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 10 | 19 |
subtype1 | 1 | 2 |
subtype2 | 0 | 4 |
subtype4 | 3 | 2 |
subtype5 | 3 | 4 |
subtype6 | 3 | 7 |
P value = 0.494 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2B | N3 |
---|---|---|---|---|---|
ALL | 15 | 2 | 4 | 1 | 4 |
subtype1 | 3 | 0 | 0 | 0 | 0 |
subtype2 | 2 | 1 | 1 | 0 | 0 |
subtype4 | 1 | 1 | 1 | 0 | 2 |
subtype5 | 3 | 0 | 1 | 1 | 0 |
subtype6 | 6 | 0 | 1 | 0 | 2 |
P value = 0.19 (Chi-square test), Q value = 1
nPatients | I OR II NOS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 3 | 2 | 3 | 3 | 2 | 1 | 1 | 1 | 3 | 5 | 1 |
subtype1 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 |
subtype4 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 1 |
subtype5 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 |
subtype6 | 1 | 0 | 1 | 1 | 2 | 0 | 1 | 1 | 0 | 0 | 2 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 15 | 12 |
P value = 0.00161 (logrank test), Q value = 0.076
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 8 | 6 | 3.5 - 28.1 (9.3) |
subtype2 | 7 | 1 | 8.4 - 48.8 (25.3) |
subtype3 | 7 | 6 | 1.1 - 15.4 (8.1) |
P value = 0.633 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 18 | 55.2 (15.5) |
subtype2 | 15 | 58.5 (15.0) |
subtype3 | 12 | 60.7 (16.5) |
P value = 0.0337 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 3 | 7 | 8 |
subtype2 | 1 | 1 | 13 |
subtype3 | 4 | 1 | 7 |
P value = 0.0833 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 9 | 9 |
subtype2 | 2 | 13 |
subtype3 | 5 | 7 |
P value = 0.881 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 10 | 2 | 1 | 1 | 1 | 2 |
subtype2 | 8 | 1 | 2 | 0 | 1 | 1 |
subtype3 | 9 | 0 | 1 | 0 | 0 | 2 |
P value = 0.629 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 0 | 1 | 1 | 3 | 1 | 1 | 2 | 1 | 0 | 1 | 3 | 2 | 1 |
subtype2 | 0 | 2 | 1 | 2 | 1 | 2 | 0 | 0 | 1 | 0 | 3 | 1 | 0 |
subtype3 | 1 | 0 | 2 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 0 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 9 | 16 | 20 |
P value = 0.00176 (logrank test), Q value = 0.081
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 6 | 6 | 1.1 - 15.4 (6.2) |
subtype2 | 7 | 2 | 8.4 - 48.8 (23.9) |
subtype3 | 9 | 5 | 3.5 - 28.1 (8.8) |
P value = 0.83 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 9 | 60.1 (18.7) |
subtype2 | 16 | 58.2 (15.2) |
subtype3 | 20 | 56.4 (14.6) |
P value = 0.00122 (Chi-square test), Q value = 0.059
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 4 | 0 | 5 |
subtype2 | 0 | 1 | 15 |
subtype3 | 4 | 8 | 8 |
P value = 0.157 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 3 | 6 |
subtype2 | 3 | 13 |
subtype3 | 10 | 10 |
P value = 0.905 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 6 | 0 | 1 | 0 | 0 | 2 |
subtype2 | 9 | 2 | 1 | 0 | 1 | 1 |
subtype3 | 12 | 1 | 2 | 1 | 1 | 2 |
P value = 0.547 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 3 | 0 |
subtype2 | 0 | 2 | 2 | 1 | 2 | 2 | 0 | 0 | 0 | 1 | 3 | 1 | 0 |
subtype3 | 0 | 1 | 1 | 4 | 1 | 1 | 3 | 1 | 1 | 0 | 3 | 2 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 6 | 15 | 15 |
P value = 0.647 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 3 | 3 | 8.1 - 16.5 (11.6) |
subtype2 | 3 | 1 | 5.4 - 28.1 (23.9) |
subtype3 | 9 | 4 | 2.4 - 42.8 (8.8) |
subtype4 | 7 | 5 | 1.1 - 48.8 (15.4) |
P value = 0.294 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 9 | 54.7 (16.0) |
subtype2 | 6 | 49.0 (16.3) |
subtype3 | 15 | 58.3 (15.1) |
subtype4 | 15 | 62.5 (14.6) |
P value = 0.423 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 2 | 1 | 6 |
subtype2 | 0 | 1 | 5 |
subtype3 | 4 | 5 | 6 |
subtype4 | 2 | 2 | 11 |
P value = 0.579 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 5 | 4 |
subtype2 | 2 | 4 |
subtype3 | 4 | 11 |
subtype4 | 5 | 10 |
P value = 0.144 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 7 | 0 | 0 | 0 | 0 | 1 |
subtype2 | 3 | 0 | 1 | 1 | 0 | 1 |
subtype3 | 10 | 1 | 3 | 0 | 0 | 0 |
subtype4 | 7 | 2 | 0 | 0 | 2 | 3 |
P value = 0.226 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 1 | 2 | 2 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
subtype2 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 |
subtype3 | 0 | 1 | 0 | 4 | 1 | 1 | 2 | 1 | 1 | 0 | 1 | 2 | 0 |
subtype4 | 0 | 0 | 1 | 1 | 1 | 2 | 2 | 0 | 0 | 1 | 3 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 9 | 31 |
P value = 0.495 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 13 | 1.1 - 48.8 (9.8) |
subtype1 | 3 | 1 | 5.4 - 28.1 (23.9) |
subtype2 | 6 | 3 | 3.5 - 42.8 (10.0) |
subtype3 | 13 | 9 | 1.1 - 48.8 (9.7) |
P value = 0.242 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 57.8 (15.4) |
subtype1 | 5 | 48.4 (18.1) |
subtype2 | 9 | 54.9 (12.6) |
subtype3 | 31 | 60.1 (15.5) |
P value = 0.58 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 8 | 9 | 28 |
subtype1 | 0 | 1 | 4 |
subtype2 | 1 | 3 | 5 |
subtype3 | 7 | 5 | 19 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 29 |
subtype1 | 2 | 3 |
subtype2 | 3 | 6 |
subtype3 | 11 | 20 |
P value = 0.151 (Chi-square test), Q value = 1
nPatients | N0 | N1A | N1B | N2A | N2B | N3 |
---|---|---|---|---|---|---|
ALL | 27 | 3 | 4 | 1 | 2 | 5 |
subtype1 | 2 | 0 | 1 | 1 | 0 | 1 |
subtype2 | 8 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 17 | 3 | 3 | 0 | 2 | 4 |
P value = 0.121 (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 | 3 | 4 | 6 | 4 | 3 | 4 | 2 | 1 | 1 | 6 | 6 | 1 |
subtype1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 |
subtype2 | 0 | 1 | 1 | 3 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 1 | 2 | 2 | 3 | 3 | 3 | 3 | 0 | 1 | 1 | 4 | 6 | 0 |
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Cluster data file = SKCM-NRAS_Hotspot_Mutants.mergedcluster.txt
-
Clinical data file = SKCM-NRAS_Hotspot_Mutants.clin.merged.picked.txt
-
Number of patients = 45
-
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.