(All_Samples 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 9 clinical features across 211 patients, 6 significant findings detected with P value < 0.05 and Q value < 0.25.
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4 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 RPPA data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'Time to Death' and 'PRIMARY.SITE.OF.DISEASE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', and 'NEOPLASM.DISEASESTAGE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
Time to Death | logrank test |
0.886 (1.00) |
0.0897 (1.00) |
0.0874 (1.00) |
0.065 (1.00) |
0.000666 (0.04) |
0.000574 (0.035) |
0.0483 (1.00) |
0.255 (1.00) |
AGE | t-test |
0.403 (1.00) |
0.151 (1.00) |
0.221 (1.00) |
0.855 (1.00) |
0.0861 (1.00) |
0.00232 (0.137) |
0.0691 (1.00) |
0.435 (1.00) |
PRIMARY SITE OF DISEASE | Chi-square test |
0.656 (1.00) |
0.479 (1.00) |
0.0322 (1.00) |
0.11 (1.00) |
2.39e-11 (1.51e-09) |
1.37e-11 (8.77e-10) |
0.0108 (0.615) |
0.0374 (1.00) |
GENDER | Fisher's exact test |
0.858 (1.00) |
0.18 (1.00) |
0.498 (1.00) |
0.861 (1.00) |
0.457 (1.00) |
0.433 (1.00) |
0.12 (1.00) |
0.358 (1.00) |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test |
0.0595 (1.00) |
0.632 (1.00) |
0.237 (1.00) |
0.794 (1.00) |
0.3 (1.00) |
1 (1.00) |
1 (1.00) |
0.295 (1.00) |
DISTANT METASTASIS | Chi-square test |
0.603 (1.00) |
0.397 (1.00) |
0.518 (1.00) |
0.498 (1.00) |
0.268 (1.00) |
0.44 (1.00) |
0.624 (1.00) |
0.966 (1.00) |
LYMPH NODE METASTASIS | Chi-square test |
0.253 (1.00) |
0.575 (1.00) |
0.0975 (1.00) |
0.294 (1.00) |
0.457 (1.00) |
0.748 (1.00) |
0.79 (1.00) |
0.396 (1.00) |
TUMOR STAGECODE | t-test | ||||||||
NEOPLASM DISEASESTAGE | Chi-square test |
0.704 (1.00) |
0.383 (1.00) |
0.211 (1.00) |
0.0732 (1.00) |
0.00776 (0.45) |
0.000426 (0.0264) |
0.195 (1.00) |
0.337 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 43 | 65 | 40 | 54 |
P value = 0.886 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 192 | 92 | 0.0 - 357.4 (40.9) |
subtype1 | 37 | 17 | 0.3 - 228.6 (43.2) |
subtype2 | 64 | 32 | 0.1 - 357.4 (45.7) |
subtype3 | 38 | 18 | 4.2 - 314.5 (35.1) |
subtype4 | 53 | 25 | 0.0 - 346.0 (35.9) |
P value = 0.403 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 198 | 56.8 (16.1) |
subtype1 | 40 | 53.2 (17.3) |
subtype2 | 65 | 58.0 (17.0) |
subtype3 | 40 | 58.7 (14.0) |
subtype4 | 53 | 56.4 (15.5) |
P value = 0.656 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 27 | 26 | 37 | 112 |
subtype1 | 6 | 8 | 8 | 21 |
subtype2 | 11 | 8 | 14 | 32 |
subtype3 | 4 | 5 | 4 | 27 |
subtype4 | 6 | 5 | 11 | 32 |
P value = 0.858 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 76 | 126 |
subtype1 | 17 | 26 |
subtype2 | 24 | 41 |
subtype3 | 13 | 27 |
subtype4 | 22 | 32 |
P value = 0.0595 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 199 |
subtype1 | 1 | 42 |
subtype2 | 0 | 65 |
subtype3 | 2 | 38 |
subtype4 | 0 | 54 |
P value = 0.603 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 176 | 2 | 2 | 2 | 3 |
subtype1 | 34 | 0 | 0 | 1 | 2 |
subtype2 | 57 | 1 | 1 | 0 | 0 |
subtype3 | 38 | 0 | 0 | 0 | 0 |
subtype4 | 47 | 1 | 1 | 1 | 1 |
P value = 0.253 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 110 | 2 | 8 | 17 | 1 | 5 | 14 | 6 | 19 | 5 |
subtype1 | 24 | 0 | 0 | 2 | 0 | 1 | 4 | 0 | 6 | 1 |
subtype2 | 36 | 0 | 5 | 8 | 0 | 1 | 3 | 2 | 5 | 0 |
subtype3 | 23 | 2 | 1 | 2 | 1 | 0 | 4 | 2 | 2 | 1 |
subtype4 | 27 | 0 | 2 | 5 | 0 | 3 | 3 | 2 | 6 | 3 |
P value = 0.704 (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 | 4 | 17 | 10 | 15 | 20 | 9 | 10 | 23 | 9 | 7 | 21 | 27 | 7 |
subtype1 | 1 | 2 | 2 | 2 | 5 | 3 | 3 | 6 | 2 | 0 | 2 | 6 | 3 |
subtype2 | 2 | 3 | 3 | 5 | 8 | 3 | 3 | 7 | 3 | 4 | 5 | 9 | 2 |
subtype3 | 0 | 8 | 1 | 4 | 2 | 3 | 2 | 3 | 3 | 0 | 6 | 5 | 0 |
subtype4 | 1 | 4 | 4 | 4 | 5 | 0 | 2 | 7 | 1 | 3 | 8 | 7 | 2 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 56 | 78 | 77 |
P value = 0.0897 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 201 | 96 | 0.0 - 357.4 (39.6) |
subtype1 | 55 | 31 | 0.1 - 204.6 (33.2) |
subtype2 | 76 | 32 | 0.0 - 357.4 (45.4) |
subtype3 | 70 | 33 | 0.5 - 346.0 (44.2) |
P value = 0.151 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 56.5 (16.0) |
subtype1 | 56 | 56.5 (16.6) |
subtype2 | 77 | 59.0 (16.2) |
subtype3 | 74 | 53.9 (15.1) |
P value = 0.479 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 29 | 28 | 38 | 116 |
subtype1 | 11 | 8 | 11 | 26 |
subtype2 | 11 | 10 | 16 | 41 |
subtype3 | 7 | 10 | 11 | 49 |
P value = 0.18 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 80 | 131 |
subtype1 | 23 | 33 |
subtype2 | 34 | 44 |
subtype3 | 23 | 54 |
P value = 0.632 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 208 |
subtype1 | 0 | 56 |
subtype2 | 1 | 77 |
subtype3 | 2 | 75 |
P value = 0.397 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 185 | 2 | 2 | 2 | 3 |
subtype1 | 49 | 1 | 1 | 0 | 0 |
subtype2 | 69 | 1 | 0 | 1 | 0 |
subtype3 | 67 | 0 | 1 | 1 | 3 |
P value = 0.575 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 114 | 3 | 9 | 17 | 1 | 5 | 15 | 6 | 21 | 5 |
subtype1 | 32 | 1 | 4 | 6 | 0 | 0 | 4 | 1 | 3 | 1 |
subtype2 | 45 | 0 | 3 | 2 | 1 | 3 | 5 | 3 | 9 | 1 |
subtype3 | 37 | 2 | 2 | 9 | 0 | 2 | 6 | 2 | 9 | 3 |
P value = 0.383 (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 | 4 | 18 | 10 | 16 | 20 | 10 | 10 | 24 | 10 | 7 | 23 | 29 | 7 |
subtype1 | 1 | 3 | 1 | 4 | 6 | 3 | 5 | 8 | 3 | 2 | 6 | 8 | 2 |
subtype2 | 3 | 4 | 6 | 6 | 5 | 4 | 4 | 12 | 2 | 4 | 7 | 10 | 1 |
subtype3 | 0 | 11 | 3 | 6 | 9 | 3 | 1 | 4 | 5 | 1 | 10 | 11 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 57 | 31 | 33 |
P value = 0.0874 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 117 | 62 | 0.0 - 357.4 (44.0) |
subtype1 | 56 | 26 | 1.4 - 357.4 (51.0) |
subtype2 | 30 | 17 | 0.4 - 182.0 (27.8) |
subtype3 | 31 | 19 | 0.0 - 346.0 (39.6) |
P value = 0.221 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 56.4 (16.4) |
subtype1 | 56 | 56.6 (16.4) |
subtype2 | 31 | 59.9 (16.1) |
subtype3 | 32 | 52.7 (16.4) |
P value = 0.0322 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 15 | 9 | 17 | 80 |
subtype1 | 5 | 4 | 3 | 45 |
subtype2 | 5 | 1 | 5 | 20 |
subtype3 | 5 | 4 | 9 | 15 |
P value = 0.498 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 46 | 75 |
subtype1 | 23 | 34 |
subtype2 | 9 | 22 |
subtype3 | 14 | 19 |
P value = 0.237 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 118 |
subtype1 | 1 | 56 |
subtype2 | 2 | 29 |
subtype3 | 0 | 33 |
P value = 0.518 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 99 | 1 | 2 | 3 |
subtype1 | 44 | 1 | 0 | 1 |
subtype2 | 27 | 0 | 1 | 0 |
subtype3 | 28 | 0 | 1 | 2 |
P value = 0.0975 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 59 | 2 | 4 | 13 | 3 | 8 | 4 | 11 | 3 |
subtype1 | 34 | 1 | 1 | 3 | 2 | 3 | 1 | 1 | 1 |
subtype2 | 11 | 0 | 0 | 6 | 1 | 4 | 2 | 4 | 1 |
subtype3 | 14 | 1 | 3 | 4 | 0 | 1 | 1 | 6 | 1 |
P value = 0.211 (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 | 3 | 11 | 8 | 9 | 10 | 5 | 5 | 6 | 6 | 3 | 13 | 15 | 5 |
subtype1 | 2 | 7 | 4 | 5 | 6 | 4 | 2 | 3 | 3 | 1 | 5 | 1 | 2 |
subtype2 | 1 | 1 | 3 | 0 | 3 | 0 | 2 | 1 | 1 | 0 | 4 | 8 | 0 |
subtype3 | 0 | 3 | 1 | 4 | 1 | 1 | 1 | 2 | 2 | 2 | 4 | 6 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 36 | 55 | 30 |
P value = 0.065 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 117 | 62 | 0.0 - 357.4 (44.0) |
subtype1 | 36 | 17 | 1.4 - 357.4 (51.2) |
subtype2 | 54 | 27 | 0.4 - 248.6 (43.3) |
subtype3 | 27 | 18 | 0.0 - 176.6 (35.9) |
P value = 0.855 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 56.4 (16.4) |
subtype1 | 36 | 56.7 (15.1) |
subtype2 | 54 | 57.0 (17.0) |
subtype3 | 29 | 54.9 (17.3) |
P value = 0.11 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 15 | 9 | 17 | 80 |
subtype1 | 2 | 2 | 4 | 28 |
subtype2 | 7 | 3 | 6 | 39 |
subtype3 | 6 | 4 | 7 | 13 |
P value = 0.861 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 46 | 75 |
subtype1 | 14 | 22 |
subtype2 | 22 | 33 |
subtype3 | 10 | 20 |
P value = 0.794 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 118 |
subtype1 | 1 | 35 |
subtype2 | 2 | 53 |
subtype3 | 0 | 30 |
P value = 0.498 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1B | M1C |
---|---|---|---|---|
ALL | 99 | 1 | 2 | 3 |
subtype1 | 26 | 0 | 1 | 1 |
subtype2 | 47 | 1 | 1 | 0 |
subtype3 | 26 | 0 | 0 | 2 |
P value = 0.294 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 59 | 2 | 4 | 13 | 3 | 8 | 4 | 11 | 3 |
subtype1 | 21 | 0 | 0 | 1 | 0 | 3 | 1 | 2 | 1 |
subtype2 | 27 | 1 | 1 | 6 | 3 | 3 | 2 | 5 | 2 |
subtype3 | 11 | 1 | 3 | 6 | 0 | 2 | 1 | 4 | 0 |
P value = 0.0732 (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 | 3 | 11 | 8 | 9 | 10 | 5 | 5 | 6 | 6 | 3 | 13 | 15 | 5 |
subtype1 | 2 | 6 | 2 | 2 | 1 | 4 | 1 | 2 | 0 | 0 | 3 | 2 | 2 |
subtype2 | 1 | 3 | 5 | 4 | 9 | 0 | 3 | 2 | 4 | 1 | 5 | 6 | 1 |
subtype3 | 0 | 2 | 1 | 3 | 0 | 1 | 1 | 2 | 2 | 2 | 5 | 7 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 32 | 56 | 60 | 50 |
P value = 0.000666 (logrank test), Q value = 0.04
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 188 | 91 | 0.0 - 357.4 (42.4) |
subtype1 | 28 | 12 | 0.0 - 76.4 (11.8) |
subtype2 | 53 | 30 | 0.1 - 228.6 (36.0) |
subtype3 | 59 | 33 | 0.4 - 357.4 (61.0) |
subtype4 | 48 | 16 | 4.2 - 203.0 (49.6) |
P value = 0.0861 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 194 | 56.6 (16.2) |
subtype1 | 32 | 57.9 (17.6) |
subtype2 | 54 | 60.0 (15.4) |
subtype3 | 59 | 52.4 (16.3) |
subtype4 | 49 | 57.2 (15.5) |
P value = 2.39e-11 (Chi-square test), Q value = 1.5e-09
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 27 | 24 | 35 | 112 |
subtype1 | 6 | 15 | 6 | 5 |
subtype2 | 8 | 6 | 6 | 36 |
subtype3 | 9 | 2 | 19 | 30 |
subtype4 | 4 | 1 | 4 | 41 |
P value = 0.457 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 75 | 123 |
subtype1 | 10 | 22 |
subtype2 | 22 | 34 |
subtype3 | 27 | 33 |
subtype4 | 16 | 34 |
P value = 0.3 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 195 |
subtype1 | 0 | 32 |
subtype2 | 1 | 55 |
subtype3 | 0 | 60 |
subtype4 | 2 | 48 |
P value = 0.268 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 172 | 2 | 2 | 2 | 3 |
subtype1 | 27 | 2 | 0 | 0 | 1 |
subtype2 | 49 | 0 | 1 | 1 | 0 |
subtype3 | 51 | 0 | 1 | 1 | 1 |
subtype4 | 45 | 0 | 0 | 0 | 1 |
P value = 0.457 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 109 | 2 | 7 | 17 | 1 | 5 | 13 | 6 | 18 | 5 |
subtype1 | 17 | 1 | 1 | 2 | 0 | 0 | 2 | 2 | 2 | 3 |
subtype2 | 32 | 0 | 2 | 6 | 0 | 3 | 4 | 0 | 6 | 0 |
subtype3 | 30 | 0 | 3 | 5 | 0 | 1 | 3 | 4 | 6 | 2 |
subtype4 | 30 | 1 | 1 | 4 | 1 | 1 | 4 | 0 | 4 | 0 |
P value = 0.00776 (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 | 4 | 17 | 10 | 15 | 20 | 9 | 10 | 22 | 9 | 6 | 20 | 26 | 7 |
subtype1 | 0 | 1 | 0 | 1 | 3 | 2 | 1 | 11 | 1 | 1 | 3 | 3 | 3 |
subtype2 | 2 | 2 | 3 | 5 | 4 | 1 | 6 | 8 | 1 | 3 | 6 | 8 | 0 |
subtype3 | 2 | 7 | 1 | 5 | 7 | 2 | 3 | 2 | 4 | 2 | 5 | 9 | 3 |
subtype4 | 0 | 7 | 6 | 4 | 6 | 4 | 0 | 1 | 3 | 0 | 6 | 6 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 59 | 77 | 62 |
P value = 0.000574 (logrank test), Q value = 0.035
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 188 | 91 | 0.0 - 357.4 (42.4) |
subtype1 | 54 | 28 | 0.0 - 228.6 (15.6) |
subtype2 | 73 | 28 | 2.7 - 203.0 (44.4) |
subtype3 | 61 | 35 | 0.4 - 357.4 (61.5) |
P value = 0.00232 (ANOVA), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 194 | 56.6 (16.2) |
subtype1 | 58 | 62.6 (15.1) |
subtype2 | 75 | 55.2 (16.5) |
subtype3 | 61 | 52.8 (15.6) |
P value = 1.37e-11 (Chi-square test), Q value = 8.8e-10
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 27 | 24 | 35 | 112 |
subtype1 | 14 | 17 | 11 | 17 |
subtype2 | 5 | 5 | 3 | 64 |
subtype3 | 8 | 2 | 21 | 31 |
P value = 0.433 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 75 | 123 |
subtype1 | 25 | 34 |
subtype2 | 25 | 52 |
subtype3 | 25 | 37 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 195 |
subtype1 | 1 | 58 |
subtype2 | 1 | 76 |
subtype3 | 1 | 61 |
P value = 0.44 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 172 | 2 | 2 | 2 | 3 |
subtype1 | 53 | 2 | 0 | 0 | 0 |
subtype2 | 67 | 0 | 1 | 1 | 2 |
subtype3 | 52 | 0 | 1 | 1 | 1 |
P value = 0.748 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 109 | 2 | 7 | 17 | 1 | 5 | 13 | 6 | 18 | 5 |
subtype1 | 35 | 0 | 1 | 5 | 0 | 0 | 5 | 2 | 5 | 3 |
subtype2 | 43 | 1 | 3 | 7 | 1 | 3 | 5 | 0 | 8 | 1 |
subtype3 | 31 | 1 | 3 | 5 | 0 | 2 | 3 | 4 | 5 | 1 |
P value = 0.000426 (Chi-square test), Q value = 0.026
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 | 4 | 17 | 10 | 15 | 20 | 9 | 10 | 22 | 9 | 6 | 20 | 26 | 7 |
subtype1 | 1 | 1 | 1 | 2 | 5 | 4 | 6 | 17 | 0 | 1 | 6 | 9 | 2 |
subtype2 | 1 | 7 | 8 | 7 | 8 | 4 | 1 | 4 | 4 | 2 | 10 | 8 | 2 |
subtype3 | 2 | 9 | 1 | 6 | 7 | 1 | 3 | 1 | 5 | 3 | 4 | 9 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 87 | 57 | 53 |
P value = 0.0483 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 187 | 90 | 0.0 - 357.4 (40.3) |
subtype1 | 83 | 41 | 0.0 - 216.9 (27.1) |
subtype2 | 53 | 30 | 0.3 - 314.5 (53.5) |
subtype3 | 51 | 19 | 0.2 - 357.4 (44.0) |
P value = 0.0691 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 193 | 56.7 (16.0) |
subtype1 | 85 | 58.4 (16.0) |
subtype2 | 55 | 52.5 (16.8) |
subtype3 | 53 | 58.2 (14.4) |
P value = 0.0108 (Chi-square test), Q value = 0.62
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 26 | 25 | 36 | 110 |
subtype1 | 12 | 16 | 10 | 49 |
subtype2 | 9 | 7 | 17 | 24 |
subtype3 | 5 | 2 | 9 | 37 |
P value = 0.12 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 73 | 124 |
subtype1 | 32 | 55 |
subtype2 | 16 | 41 |
subtype3 | 25 | 28 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 194 |
subtype1 | 1 | 86 |
subtype2 | 1 | 56 |
subtype3 | 1 | 52 |
P value = 0.624 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 171 | 2 | 2 | 2 | 3 |
subtype1 | 78 | 1 | 1 | 1 | 0 |
subtype2 | 52 | 0 | 0 | 0 | 2 |
subtype3 | 41 | 1 | 1 | 1 | 1 |
P value = 0.79 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 107 | 2 | 8 | 17 | 1 | 5 | 14 | 6 | 17 | 5 |
subtype1 | 50 | 1 | 2 | 9 | 0 | 3 | 7 | 2 | 7 | 1 |
subtype2 | 32 | 1 | 4 | 4 | 1 | 0 | 5 | 2 | 3 | 2 |
subtype3 | 25 | 0 | 2 | 4 | 0 | 2 | 2 | 2 | 7 | 2 |
P value = 0.195 (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 | 4 | 17 | 10 | 15 | 19 | 8 | 10 | 22 | 9 | 7 | 21 | 25 | 7 |
subtype1 | 1 | 4 | 5 | 5 | 11 | 4 | 7 | 13 | 2 | 3 | 10 | 11 | 2 |
subtype2 | 1 | 8 | 1 | 8 | 3 | 3 | 2 | 6 | 6 | 3 | 3 | 7 | 2 |
subtype3 | 2 | 5 | 4 | 2 | 5 | 1 | 1 | 3 | 1 | 1 | 8 | 7 | 3 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 126 | 71 |
P value = 0.255 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 187 | 90 | 0.0 - 357.4 (40.3) |
subtype1 | 118 | 56 | 0.0 - 314.5 (36.0) |
subtype2 | 69 | 34 | 0.2 - 357.4 (47.8) |
P value = 0.435 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 193 | 56.7 (16.0) |
subtype1 | 123 | 57.3 (16.5) |
subtype2 | 70 | 55.5 (15.0) |
P value = 0.0374 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | PRIMARY TUMOR | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|---|
ALL | 26 | 25 | 36 | 110 |
subtype1 | 17 | 22 | 19 | 68 |
subtype2 | 9 | 3 | 17 | 42 |
P value = 0.358 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 73 | 124 |
subtype1 | 50 | 76 |
subtype2 | 23 | 48 |
P value = 0.295 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 3 | 194 |
subtype1 | 1 | 125 |
subtype2 | 2 | 69 |
P value = 0.966 (Chi-square test), Q value = 1
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 171 | 2 | 2 | 2 | 3 |
subtype1 | 111 | 1 | 1 | 1 | 2 |
subtype2 | 60 | 1 | 1 | 1 | 1 |
P value = 0.396 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 107 | 2 | 8 | 17 | 1 | 5 | 14 | 6 | 17 | 5 |
subtype1 | 76 | 1 | 5 | 10 | 0 | 3 | 10 | 2 | 8 | 3 |
subtype2 | 31 | 1 | 3 | 7 | 1 | 2 | 4 | 4 | 9 | 2 |
P value = 0.337 (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 | 4 | 17 | 10 | 15 | 19 | 8 | 10 | 22 | 9 | 7 | 21 | 25 | 7 |
subtype1 | 2 | 9 | 8 | 11 | 14 | 5 | 8 | 18 | 3 | 4 | 13 | 13 | 4 |
subtype2 | 2 | 8 | 2 | 4 | 5 | 3 | 2 | 4 | 6 | 3 | 8 | 12 | 3 |
-
Cluster data file = SKCM-All_Samples.mergedcluster.txt
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Clinical data file = SKCM-All_Samples.clin.merged.picked.txt
-
Number of patients = 211
-
Number of clustering approaches = 8
-
Number of selected clinical features = 9
-
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.