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 80 patients, 10 significant findings detected with P value < 0.05 and Q value < 0.25.
-
6 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death'.
-
4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'Time to Death'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'PATHOLOGIC_STAGE'.
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6 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death'.
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7 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'Time to Death' and 'YEARS_TO_BIRTH'.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
7.12e-05 (0.000498) |
0.0805 (0.237) |
0.225 (0.34) |
0.393 (0.5) |
0.0902 (0.237) |
0.983 (1.00) |
0.121 (0.238) |
METHLYATION CNMF |
2.71e-07 (7.59e-06) |
0.0815 (0.237) |
0.352 (0.458) |
0.603 (0.719) |
0.181 (0.315) |
0.172 (0.311) |
0.773 (0.848) |
RNAseq CNMF subtypes |
3.45e-06 (3.22e-05) |
0.331 (0.45) |
0.0545 (0.237) |
0.0548 (0.237) |
0.0701 (0.237) |
0.658 (0.768) |
0.894 (0.945) |
RNAseq cHierClus subtypes |
2.56e-08 (1.43e-06) |
0.0852 (0.237) |
0.0407 (0.228) |
0.116 (0.238) |
0.0651 (0.237) |
0.878 (0.945) |
1 (1.00) |
MIRSEQ CNMF |
2.18e-06 (2.67e-05) |
0.111 (0.238) |
0.31 (0.445) |
0.127 (0.238) |
0.28 (0.412) |
0.715 (0.817) |
0.753 (0.844) |
MIRSEQ CHIERARCHICAL |
2.38e-06 (2.67e-05) |
0.125 (0.238) |
0.192 (0.315) |
0.0974 (0.237) |
0.12 (0.238) |
0.199 (0.318) |
1 (1.00) |
MIRseq Mature CNMF subtypes |
5.15e-07 (9.62e-06) |
0.00434 (0.027) |
0.191 (0.315) |
0.11 (0.238) |
0.0968 (0.237) |
0.0575 (0.237) |
0.338 (0.45) |
MIRseq Mature cHierClus subtypes |
4.33e-06 (3.46e-05) |
0.0762 (0.237) |
0.216 (0.336) |
0.335 (0.45) |
0.0779 (0.237) |
0.518 (0.63) |
0.425 (0.529) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 22 | 7 | 10 | 31 | 6 | 4 |
P value = 7.12e-05 (logrank test), Q value = 5e-04
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 22 | 7 | 0.1 - 82.2 (26.2) |
subtype2 | 7 | 4 | 2.7 - 24.0 (13.6) |
subtype3 | 10 | 6 | 13.1 - 45.9 (19.8) |
subtype4 | 31 | 2 | 0.2 - 85.5 (33.8) |
subtype5 | 6 | 2 | 1.4 - 36.6 (30.5) |
subtype6 | 4 | 2 | 1.6 - 43.2 (23.0) |
P value = 0.0805 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 22 | 60.5 (11.0) |
subtype2 | 7 | 72.6 (12.2) |
subtype3 | 10 | 65.5 (15.3) |
subtype4 | 31 | 57.5 (14.7) |
subtype5 | 6 | 61.3 (14.7) |
subtype6 | 4 | 71.8 (10.2) |
P value = 0.225 (Fisher's exact test), Q value = 0.34
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 1 | 7 | 9 | 3 | 0 | 2 |
subtype2 | 0 | 1 | 2 | 1 | 1 | 2 |
subtype3 | 2 | 4 | 2 | 2 | 0 | 0 |
subtype4 | 7 | 13 | 8 | 3 | 0 | 0 |
subtype5 | 1 | 2 | 3 | 0 | 0 | 0 |
subtype6 | 1 | 0 | 1 | 1 | 0 | 0 |
P value = 0.393 (Fisher's exact test), Q value = 0.5
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 2 | 9 | 11 |
subtype2 | 1 | 0 | 6 |
subtype3 | 2 | 4 | 4 |
subtype4 | 7 | 14 | 10 |
subtype5 | 1 | 3 | 2 |
subtype6 | 1 | 2 | 1 |
P value = 0.0902 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 12 | 2 |
subtype2 | 4 | 2 |
subtype3 | 6 | 0 |
subtype4 | 22 | 0 |
subtype5 | 4 | 0 |
subtype6 | 3 | 0 |
P value = 0.983 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 11 | 11 |
subtype2 | 3 | 4 |
subtype3 | 4 | 6 |
subtype4 | 13 | 18 |
subtype5 | 2 | 4 |
subtype6 | 2 | 2 |
P value = 0.121 (Fisher's exact test), Q value = 0.24
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 21 | 0 |
subtype2 | 6 | 1 |
subtype3 | 10 | 0 |
subtype4 | 30 | 1 |
subtype5 | 6 | 0 |
subtype6 | 3 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 28 | 14 | 14 | 24 |
P value = 2.71e-07 (logrank test), Q value = 7.6e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 28 | 17 | 0.1 - 45.3 (19.3) |
subtype2 | 14 | 1 | 0.2 - 85.5 (34.2) |
subtype3 | 14 | 3 | 1.3 - 82.2 (24.8) |
subtype4 | 24 | 2 | 0.2 - 46.8 (27.1) |
P value = 0.0815 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 28 | 66.9 (12.1) |
subtype2 | 14 | 60.2 (12.6) |
subtype3 | 14 | 61.9 (13.4) |
subtype4 | 24 | 56.2 (15.5) |
P value = 0.352 (Fisher's exact test), Q value = 0.46
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 1 | 10 | 8 | 3 | 1 | 4 |
subtype2 | 2 | 4 | 6 | 2 | 0 | 0 |
subtype3 | 3 | 3 | 6 | 2 | 0 | 0 |
subtype4 | 6 | 10 | 5 | 3 | 0 | 0 |
P value = 0.603 (Fisher's exact test), Q value = 0.72
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 2 | 11 | 15 |
subtype2 | 3 | 5 | 6 |
subtype3 | 3 | 6 | 5 |
subtype4 | 6 | 10 | 8 |
P value = 0.181 (Fisher's exact test), Q value = 0.32
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 18 | 4 |
subtype2 | 8 | 0 |
subtype3 | 9 | 0 |
subtype4 | 16 | 0 |
P value = 0.172 (Fisher's exact test), Q value = 0.31
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 11 | 17 |
subtype2 | 5 | 9 |
subtype3 | 10 | 4 |
subtype4 | 9 | 15 |
P value = 0.773 (Fisher's exact test), Q value = 0.85
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 25 | 2 |
subtype2 | 14 | 0 |
subtype3 | 14 | 0 |
subtype4 | 23 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 18 | 15 | 32 | 15 |
P value = 3.45e-06 (logrank test), Q value = 3.2e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 18 | 9 | 1.3 - 49.7 (14.9) |
subtype2 | 15 | 5 | 0.4 - 61.2 (27.5) |
subtype3 | 32 | 1 | 0.2 - 85.5 (36.4) |
subtype4 | 15 | 8 | 0.1 - 45.3 (22.0) |
P value = 0.331 (Kruskal-Wallis (anova)), Q value = 0.45
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 18 | 67.2 (14.3) |
subtype2 | 15 | 61.0 (13.1) |
subtype3 | 32 | 59.0 (14.4) |
subtype4 | 15 | 61.4 (12.8) |
P value = 0.0545 (Fisher's exact test), Q value = 0.24
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 2 | 2 | 7 | 3 | 1 | 3 |
subtype2 | 0 | 6 | 5 | 3 | 0 | 0 |
subtype3 | 9 | 12 | 8 | 3 | 0 | 0 |
subtype4 | 1 | 7 | 5 | 1 | 0 | 1 |
P value = 0.0548 (Fisher's exact test), Q value = 0.24
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 2 | 3 | 13 |
subtype2 | 2 | 8 | 5 |
subtype3 | 9 | 14 | 9 |
subtype4 | 1 | 7 | 7 |
P value = 0.0701 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 12 | 3 |
subtype2 | 10 | 0 |
subtype3 | 20 | 0 |
subtype4 | 9 | 1 |
P value = 0.658 (Fisher's exact test), Q value = 0.77
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 9 | 9 |
subtype2 | 8 | 7 |
subtype3 | 13 | 19 |
subtype4 | 5 | 10 |
P value = 0.894 (Fisher's exact test), Q value = 0.95
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 16 | 1 |
subtype2 | 14 | 1 |
subtype3 | 31 | 1 |
subtype4 | 15 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 29 | 33 | 18 |
P value = 2.56e-08 (logrank test), Q value = 1.4e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 29 | 17 | 0.1 - 49.7 (15.4) |
subtype2 | 33 | 1 | 0.2 - 85.5 (33.8) |
subtype3 | 18 | 5 | 0.4 - 61.2 (29.3) |
P value = 0.0852 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 29 | 66.4 (12.5) |
subtype2 | 33 | 57.8 (14.5) |
subtype3 | 18 | 60.9 (13.4) |
P value = 0.0407 (Fisher's exact test), Q value = 0.23
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 3 | 9 | 9 | 3 | 1 | 4 |
subtype2 | 9 | 13 | 8 | 3 | 0 | 0 |
subtype3 | 0 | 5 | 8 | 4 | 0 | 0 |
P value = 0.116 (Fisher's exact test), Q value = 0.24
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 4 | 9 | 16 |
subtype2 | 9 | 15 | 9 |
subtype3 | 1 | 8 | 9 |
P value = 0.0651 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 18 | 4 |
subtype2 | 22 | 0 |
subtype3 | 11 | 0 |
P value = 0.878 (Fisher's exact test), Q value = 0.95
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 12 | 17 |
subtype2 | 14 | 19 |
subtype3 | 9 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 27 | 1 |
subtype2 | 32 | 1 |
subtype3 | 17 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 8 | 8 | 11 | 25 | 23 | 5 |
P value = 2.18e-06 (logrank test), Q value = 2.7e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 8 | 3 | 1.4 - 45.9 (33.3) |
subtype2 | 8 | 3 | 7.9 - 61.2 (33.3) |
subtype3 | 11 | 0 | 0.2 - 85.5 (31.8) |
subtype4 | 25 | 1 | 0.2 - 82.2 (27.0) |
subtype5 | 23 | 14 | 0.1 - 45.3 (18.9) |
subtype6 | 5 | 2 | 1.3 - 49.7 (20.9) |
P value = 0.111 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 8 | 56.9 (16.2) |
subtype2 | 8 | 64.5 (11.6) |
subtype3 | 11 | 57.4 (11.3) |
subtype4 | 25 | 57.6 (15.9) |
subtype5 | 23 | 66.9 (11.5) |
subtype6 | 5 | 70.2 (10.7) |
P value = 0.31 (Fisher's exact test), Q value = 0.44
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 0 | 4 | 2 | 1 | 0 | 1 |
subtype2 | 0 | 2 | 3 | 2 | 0 | 0 |
subtype3 | 0 | 4 | 6 | 1 | 0 | 0 |
subtype4 | 9 | 8 | 5 | 3 | 0 | 0 |
subtype5 | 2 | 7 | 8 | 2 | 1 | 3 |
subtype6 | 1 | 2 | 1 | 1 | 0 | 0 |
P value = 0.127 (Fisher's exact test), Q value = 0.24
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 1 | 4 | 3 |
subtype2 | 1 | 4 | 3 |
subtype3 | 0 | 4 | 7 |
subtype4 | 9 | 10 | 6 |
subtype5 | 2 | 7 | 14 |
subtype6 | 1 | 3 | 1 |
P value = 0.28 (Fisher's exact test), Q value = 0.41
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 4 | 1 |
subtype2 | 3 | 0 |
subtype3 | 9 | 0 |
subtype4 | 17 | 0 |
subtype5 | 14 | 3 |
subtype6 | 4 | 0 |
P value = 0.715 (Fisher's exact test), Q value = 0.82
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 5 | 3 |
subtype2 | 3 | 5 |
subtype3 | 4 | 7 |
subtype4 | 12 | 13 |
subtype5 | 8 | 15 |
subtype6 | 3 | 2 |
P value = 0.753 (Fisher's exact test), Q value = 0.84
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 7 | 0 |
subtype2 | 7 | 1 |
subtype3 | 11 | 0 |
subtype4 | 24 | 1 |
subtype5 | 22 | 1 |
subtype6 | 5 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 17 | 13 | 28 | 22 |
P value = 2.38e-06 (logrank test), Q value = 2.7e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 23 | 0.1 - 85.5 (25.8) |
subtype1 | 17 | 7 | 1.4 - 61.2 (28.7) |
subtype2 | 13 | 1 | 0.2 - 85.5 (37.8) |
subtype3 | 28 | 2 | 0.2 - 82.2 (26.8) |
subtype4 | 22 | 13 | 0.1 - 49.7 (14.3) |
P value = 0.125 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 17 | 60.9 (14.9) |
subtype2 | 13 | 59.2 (12.2) |
subtype3 | 28 | 58.4 (15.7) |
subtype4 | 22 | 67.8 (10.2) |
P value = 0.192 (Fisher's exact test), Q value = 0.32
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 1 | 7 | 5 | 1 | 1 | 1 |
subtype2 | 0 | 6 | 5 | 2 | 0 | 0 |
subtype3 | 9 | 8 | 7 | 4 | 0 | 0 |
subtype4 | 2 | 6 | 8 | 3 | 0 | 3 |
P value = 0.0974 (Fisher's exact test), Q value = 0.24
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 3 | 9 | 5 |
subtype2 | 0 | 6 | 7 |
subtype3 | 9 | 10 | 9 |
subtype4 | 2 | 7 | 13 |
P value = 0.12 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 10 | 1 |
subtype2 | 9 | 0 |
subtype3 | 19 | 0 |
subtype4 | 13 | 3 |
P value = 0.199 (Fisher's exact test), Q value = 0.32
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 10 | 7 |
subtype2 | 3 | 10 |
subtype3 | 14 | 14 |
subtype4 | 8 | 14 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 15 | 1 |
subtype2 | 13 | 0 |
subtype3 | 27 | 1 |
subtype4 | 21 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 20 | 7 | 17 | 9 | 8 | 7 | 6 |
P value = 5.15e-07 (logrank test), Q value = 9.6e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 23 | 0.1 - 85.5 (25.0) |
subtype1 | 20 | 14 | 0.1 - 41.7 (16.9) |
subtype2 | 7 | 2 | 0.4 - 61.2 (36.6) |
subtype3 | 17 | 1 | 14.0 - 85.5 (38.7) |
subtype4 | 9 | 1 | 2.1 - 41.0 (35.4) |
subtype5 | 8 | 1 | 1.6 - 56.0 (24.3) |
subtype6 | 7 | 1 | 0.2 - 27.6 (19.7) |
subtype7 | 6 | 3 | 1.3 - 46.8 (35.8) |
P value = 0.00434 (Kruskal-Wallis (anova)), Q value = 0.027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 74 | 61.9 (14.1) |
subtype1 | 20 | 66.7 (13.1) |
subtype2 | 7 | 58.7 (17.0) |
subtype3 | 17 | 52.3 (15.5) |
subtype4 | 9 | 54.4 (9.1) |
subtype5 | 8 | 69.4 (10.2) |
subtype6 | 7 | 71.0 (7.4) |
subtype7 | 6 | 67.8 (6.5) |
P value = 0.191 (Fisher's exact test), Q value = 0.32
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 10 | 25 | 24 | 9 | 1 | 4 |
subtype1 | 1 | 6 | 8 | 1 | 1 | 3 |
subtype2 | 0 | 4 | 1 | 1 | 0 | 0 |
subtype3 | 2 | 7 | 6 | 2 | 0 | 0 |
subtype4 | 0 | 1 | 5 | 3 | 0 | 0 |
subtype5 | 3 | 2 | 3 | 0 | 0 | 0 |
subtype6 | 2 | 3 | 1 | 1 | 0 | 0 |
subtype7 | 2 | 2 | 0 | 1 | 0 | 1 |
P value = 0.11 (Fisher's exact test), Q value = 0.24
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 12 | 30 | 32 |
subtype1 | 1 | 7 | 12 |
subtype2 | 2 | 4 | 1 |
subtype3 | 2 | 8 | 7 |
subtype4 | 0 | 2 | 7 |
subtype5 | 3 | 4 | 1 |
subtype6 | 2 | 3 | 2 |
subtype7 | 2 | 2 | 2 |
P value = 0.0968 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 48 | 4 |
subtype1 | 14 | 3 |
subtype2 | 4 | 0 |
subtype3 | 14 | 0 |
subtype4 | 5 | 0 |
subtype5 | 7 | 0 |
subtype6 | 4 | 0 |
subtype7 | 0 | 1 |
P value = 0.0575 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 42 |
subtype1 | 9 | 11 |
subtype2 | 3 | 4 |
subtype3 | 4 | 13 |
subtype4 | 2 | 7 |
subtype5 | 7 | 1 |
subtype6 | 3 | 4 |
subtype7 | 4 | 2 |
P value = 0.338 (Fisher's exact test), Q value = 0.45
nPatients | NO | YES |
---|---|---|
ALL | 70 | 3 |
subtype1 | 18 | 1 |
subtype2 | 6 | 1 |
subtype3 | 17 | 0 |
subtype4 | 9 | 0 |
subtype5 | 8 | 0 |
subtype6 | 6 | 1 |
subtype7 | 6 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 18 | 28 | 16 | 12 |
P value = 4.33e-06 (logrank test), Q value = 3.5e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 23 | 0.1 - 85.5 (25.0) |
subtype1 | 18 | 9 | 1.4 - 61.2 (23.7) |
subtype2 | 28 | 2 | 0.2 - 85.5 (30.7) |
subtype3 | 16 | 10 | 0.1 - 49.7 (14.3) |
subtype4 | 12 | 2 | 0.4 - 45.9 (29.6) |
P value = 0.0762 (Kruskal-Wallis (anova)), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 74 | 61.9 (14.1) |
subtype1 | 18 | 64.1 (12.5) |
subtype2 | 28 | 59.2 (15.4) |
subtype3 | 16 | 68.8 (11.6) |
subtype4 | 12 | 55.9 (13.7) |
P value = 0.216 (Fisher's exact test), Q value = 0.34
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 10 | 25 | 24 | 9 | 1 | 4 |
subtype1 | 1 | 3 | 7 | 3 | 1 | 2 |
subtype2 | 7 | 11 | 7 | 3 | 0 | 0 |
subtype3 | 2 | 7 | 4 | 1 | 0 | 2 |
subtype4 | 0 | 4 | 6 | 2 | 0 | 0 |
P value = 0.335 (Fisher's exact test), Q value = 0.45
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 12 | 30 | 32 |
subtype1 | 2 | 6 | 10 |
subtype2 | 7 | 13 | 8 |
subtype3 | 2 | 8 | 6 |
subtype4 | 1 | 3 | 8 |
P value = 0.0779 (Fisher's exact test), Q value = 0.24
nPatients | 0 | 1 |
---|---|---|
ALL | 48 | 4 |
subtype1 | 10 | 2 |
subtype2 | 21 | 0 |
subtype3 | 10 | 2 |
subtype4 | 7 | 0 |
P value = 0.518 (Fisher's exact test), Q value = 0.63
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 42 |
subtype1 | 6 | 12 |
subtype2 | 11 | 17 |
subtype3 | 8 | 8 |
subtype4 | 7 | 5 |
P value = 0.425 (Fisher's exact test), Q value = 0.53
nPatients | NO | YES |
---|---|---|
ALL | 70 | 3 |
subtype1 | 15 | 2 |
subtype2 | 27 | 1 |
subtype3 | 16 | 0 |
subtype4 | 12 | 0 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UVM-TP/22507229/UVM-TP.merged_data.txt
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Number of patients = 80
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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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.