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, 13 significant findings detected with P value < 0.05 and Q value < 0.25.
-
3 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'YEARS_TO_BIRTH', and 'PATHOLOGY_M_STAGE'.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'PATHOLOGY_M_STAGE'.
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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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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death'.
-
4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'Time to Death'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'Time to Death' and 'PATHOLOGY_M_STAGE'.
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6 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 |
0.00172 (0.0161) |
0.0498 (0.212) |
0.0735 (0.248) |
0.468 (0.582) |
0.0482 (0.212) |
0.919 (0.953) |
0.342 (0.479) |
METHLYATION CNMF |
0.000778 (0.00872) |
0.166 (0.32) |
0.165 (0.32) |
0.265 (0.391) |
0.11 (0.274) |
0.503 (0.612) |
0.789 (0.857) |
RNAseq CNMF subtypes |
1.66e-05 (0.000466) |
0.198 (0.324) |
0.105 (0.274) |
0.131 (0.282) |
0.0376 (0.211) |
0.699 (0.799) |
0.781 (0.857) |
RNAseq cHierClus subtypes |
1.04e-05 (0.000466) |
0.0852 (0.259) |
0.0414 (0.211) |
0.114 (0.274) |
0.0645 (0.241) |
0.878 (0.927) |
1 (1.00) |
MIRSEQ CNMF |
0.0271 (0.168) |
0.559 (0.666) |
0.0878 (0.259) |
0.203 (0.324) |
0.181 (0.324) |
0.189 (0.324) |
0.796 (0.857) |
MIRSEQ CHIERARCHICAL |
4.13e-05 (0.000771) |
0.125 (0.28) |
0.192 (0.324) |
0.0964 (0.27) |
0.117 (0.274) |
0.2 (0.324) |
1 (1.00) |
MIRseq Mature CNMF subtypes |
0.00411 (0.0328) |
0.053 (0.212) |
0.138 (0.287) |
0.318 (0.457) |
0.0231 (0.162) |
0.0754 (0.248) |
0.406 (0.528) |
MIRseq Mature cHierClus subtypes |
6.34e-05 (0.000888) |
0.42 (0.535) |
0.208 (0.324) |
0.394 (0.525) |
0.235 (0.356) |
0.381 (0.52) |
0.677 (0.79) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 22 | 36 | 22 |
P value = 0.00172 (logrank test), Q value = 0.016
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 22 | 5 | 0.1 - 31.4 (16.2) |
subtype2 | 36 | 1 | 0.1 - 85.5 (23.2) |
subtype3 | 22 | 8 | 0.3 - 52.6 (14.0) |
P value = 0.0498 (Kruskal-Wallis (anova)), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 22 | 65.0 (12.5) |
subtype2 | 36 | 57.1 (14.3) |
subtype3 | 22 | 65.7 (13.1) |
P value = 0.0735 (Fisher's exact test), Q value = 0.25
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 1 | 8 | 5 | 3 | 1 | 3 |
subtype2 | 9 | 14 | 9 | 4 | 0 | 0 |
subtype3 | 2 | 5 | 11 | 3 | 0 | 1 |
P value = 0.468 (Fisher's exact test), Q value = 0.58
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 2 | 8 | 12 |
subtype2 | 9 | 15 | 12 |
subtype3 | 3 | 9 | 10 |
P value = 0.0482 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 13 | 3 |
subtype2 | 25 | 0 |
subtype3 | 13 | 1 |
P value = 0.919 (Fisher's exact test), Q value = 0.95
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 10 | 12 |
subtype2 | 15 | 21 |
subtype3 | 10 | 12 |
P value = 0.342 (Fisher's exact test), Q value = 0.48
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 19 | 2 |
subtype2 | 35 | 1 |
subtype3 | 22 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 33 | 18 | 29 |
P value = 0.000778 (logrank test), Q value = 0.0087
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 33 | 11 | 0.1 - 45.9 (15.0) |
subtype2 | 18 | 2 | 0.2 - 74.5 (19.6) |
subtype3 | 29 | 1 | 0.1 - 85.5 (24.4) |
P value = 0.166 (Kruskal-Wallis (anova)), Q value = 0.32
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 33 | 65.2 (13.2) |
subtype2 | 18 | 61.9 (11.9) |
subtype3 | 29 | 57.4 (15.2) |
P value = 0.165 (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 | 2 | 11 | 11 | 3 | 1 | 4 |
subtype2 | 2 | 5 | 7 | 4 | 0 | 0 |
subtype3 | 8 | 11 | 7 | 3 | 0 | 0 |
P value = 0.265 (Fisher's exact test), Q value = 0.39
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 3 | 12 | 18 |
subtype2 | 3 | 8 | 7 |
subtype3 | 8 | 12 | 9 |
P value = 0.11 (Fisher's exact test), Q value = 0.27
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 20 | 4 |
subtype2 | 13 | 0 |
subtype3 | 18 | 0 |
P value = 0.503 (Fisher's exact test), Q value = 0.61
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 14 | 19 |
subtype2 | 10 | 8 |
subtype3 | 11 | 18 |
P value = 0.789 (Fisher's exact test), Q value = 0.86
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 30 | 2 |
subtype2 | 18 | 0 |
subtype3 | 28 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 30 | 15 | 35 |
P value = 1.66e-05 (logrank test), Q value = 0.00047
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 30 | 11 | 0.1 - 37.8 (13.4) |
subtype2 | 15 | 2 | 0.2 - 52.6 (21.0) |
subtype3 | 35 | 1 | 0.1 - 85.5 (22.0) |
P value = 0.198 (Kruskal-Wallis (anova)), Q value = 0.32
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 30 | 65.5 (13.2) |
subtype2 | 15 | 61.0 (13.1) |
subtype3 | 35 | 58.6 (14.5) |
P value = 0.105 (Fisher's exact test), Q value = 0.27
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 3 | 8 | 11 | 3 | 1 | 4 |
subtype2 | 0 | 6 | 5 | 3 | 0 | 0 |
subtype3 | 9 | 13 | 9 | 4 | 0 | 0 |
P value = 0.131 (Fisher's exact test), Q value = 0.28
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 3 | 9 | 18 |
subtype2 | 2 | 8 | 5 |
subtype3 | 9 | 15 | 11 |
P value = 0.0376 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 18 | 4 |
subtype2 | 10 | 0 |
subtype3 | 23 | 0 |
P value = 0.699 (Fisher's exact test), Q value = 0.8
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 13 | 17 |
subtype2 | 8 | 7 |
subtype3 | 14 | 21 |
P value = 0.781 (Fisher's exact test), Q value = 0.86
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 28 | 1 |
subtype2 | 14 | 1 |
subtype3 | 34 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 29 | 33 | 18 |
P value = 1.04e-05 (logrank test), Q value = 0.00047
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 29 | 11 | 0.1 - 37.8 (13.6) |
subtype2 | 33 | 1 | 0.1 - 85.5 (24.4) |
subtype3 | 18 | 2 | 0.2 - 52.6 (20.3) |
P value = 0.0852 (Kruskal-Wallis (anova)), Q value = 0.26
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 = 0.0414 (Fisher's exact test), Q value = 0.21
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 = 0.114 (Fisher's exact test), Q value = 0.27
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 4 | 9 | 16 |
subtype2 | 9 | 15 | 9 |
subtype3 | 1 | 8 | 9 |
P value = 0.0645 (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 = 0.93
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 |
---|---|---|---|
Number of samples | 34 | 17 | 29 |
P value = 0.0271 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 34 | 8 | 0.1 - 52.6 (17.5) |
subtype2 | 17 | 5 | 0.1 - 85.5 (15.0) |
subtype3 | 29 | 1 | 0.2 - 74.5 (20.2) |
P value = 0.559 (Kruskal-Wallis (anova)), Q value = 0.67
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
subtype1 | 34 | 63.2 (12.4) |
subtype2 | 17 | 63.6 (14.2) |
subtype3 | 29 | 58.7 (15.5) |
P value = 0.0878 (Fisher's exact test), Q value = 0.26
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 12 | 27 | 25 | 10 | 1 | 4 |
subtype1 | 1 | 14 | 10 | 5 | 1 | 2 |
subtype2 | 2 | 5 | 7 | 1 | 0 | 2 |
subtype3 | 9 | 8 | 8 | 4 | 0 | 0 |
P value = 0.203 (Fisher's exact test), Q value = 0.32
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 14 | 32 | 34 |
subtype1 | 3 | 16 | 15 |
subtype2 | 2 | 6 | 9 |
subtype3 | 9 | 10 | 10 |
P value = 0.181 (Fisher's exact test), Q value = 0.32
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 22 | 2 |
subtype2 | 9 | 2 |
subtype3 | 20 | 0 |
P value = 0.189 (Fisher's exact test), Q value = 0.32
nPatients | FEMALE | MALE |
---|---|---|
ALL | 35 | 45 |
subtype1 | 11 | 23 |
subtype2 | 10 | 7 |
subtype3 | 14 | 15 |
P value = 0.796 (Fisher's exact test), Q value = 0.86
nPatients | NO | YES |
---|---|---|
ALL | 76 | 3 |
subtype1 | 31 | 2 |
subtype2 | 17 | 0 |
subtype3 | 28 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 17 | 13 | 28 | 22 |
P value = 4.13e-05 (logrank test), Q value = 0.00077
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 17 | 3 | 1.4 - 52.6 (21.7) |
subtype2 | 13 | 0 | 0.1 - 85.5 (22.0) |
subtype3 | 28 | 2 | 0.2 - 74.5 (20.0) |
subtype4 | 22 | 9 | 0.1 - 37.8 (12.9) |
P value = 0.125 (Kruskal-Wallis (anova)), Q value = 0.28
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 = 0.0964 (Fisher's exact test), Q value = 0.27
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 = 0.117 (Fisher's exact test), Q value = 0.27
nPatients | 0 | 1 |
---|---|---|
ALL | 51 | 4 |
subtype1 | 10 | 1 |
subtype2 | 9 | 0 |
subtype3 | 19 | 0 |
subtype4 | 13 | 3 |
P value = 0.2 (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 |
---|---|---|---|
Number of samples | 32 | 28 | 14 |
P value = 0.00411 (logrank test), Q value = 0.033
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 32 | 9 | 0.1 - 52.6 (14.5) |
subtype2 | 28 | 1 | 0.1 - 85.5 (23.2) |
subtype3 | 14 | 4 | 0.5 - 37.8 (13.2) |
P value = 0.053 (Kruskal-Wallis (anova)), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 74 | 61.9 (14.1) |
subtype1 | 32 | 63.2 (13.6) |
subtype2 | 28 | 57.0 (15.4) |
subtype3 | 14 | 68.9 (9.2) |
P value = 0.138 (Fisher's exact test), Q value = 0.29
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 10 | 25 | 24 | 9 | 1 | 4 |
subtype1 | 1 | 12 | 11 | 4 | 1 | 2 |
subtype2 | 4 | 10 | 10 | 4 | 0 | 0 |
subtype3 | 5 | 3 | 3 | 1 | 0 | 2 |
P value = 0.318 (Fisher's exact test), Q value = 0.46
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 12 | 30 | 32 |
subtype1 | 3 | 14 | 15 |
subtype2 | 4 | 11 | 13 |
subtype3 | 5 | 5 | 4 |
P value = 0.0231 (Fisher's exact test), Q value = 0.16
nPatients | 0 | 1 |
---|---|---|
ALL | 48 | 4 |
subtype1 | 20 | 2 |
subtype2 | 23 | 0 |
subtype3 | 5 | 2 |
P value = 0.0754 (Fisher's exact test), Q value = 0.25
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 42 |
subtype1 | 12 | 20 |
subtype2 | 10 | 18 |
subtype3 | 10 | 4 |
P value = 0.406 (Fisher's exact test), Q value = 0.53
nPatients | NO | YES |
---|---|---|
ALL | 70 | 3 |
subtype1 | 29 | 2 |
subtype2 | 28 | 0 |
subtype3 | 13 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 5 | 12 | 16 | 16 | 15 | 10 |
P value = 6.34e-05 (logrank test), Q value = 0.00089
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 74 | 14 | 0.1 - 85.5 (19.1) |
subtype1 | 5 | 2 | 1.4 - 23.3 (7.9) |
subtype2 | 12 | 1 | 0.3 - 52.6 (20.3) |
subtype3 | 16 | 0 | 0.1 - 85.5 (23.2) |
subtype4 | 16 | 1 | 0.2 - 74.5 (23.6) |
subtype5 | 15 | 6 | 0.1 - 37.8 (13.1) |
subtype6 | 10 | 4 | 1.2 - 28.4 (18.1) |
P value = 0.42 (Kruskal-Wallis (anova)), Q value = 0.54
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 74 | 61.9 (14.1) |
subtype1 | 5 | 68.2 (18.8) |
subtype2 | 12 | 60.3 (13.3) |
subtype3 | 16 | 58.2 (13.7) |
subtype4 | 16 | 60.3 (17.4) |
subtype5 | 15 | 67.9 (11.3) |
subtype6 | 10 | 60.3 (10.6) |
P value = 0.208 (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 | 0 | 1 | 2 | 0 | 1 | 1 |
subtype2 | 0 | 5 | 3 | 3 | 0 | 0 |
subtype3 | 3 | 5 | 7 | 1 | 0 | 0 |
subtype4 | 5 | 6 | 3 | 2 | 0 | 0 |
subtype5 | 1 | 7 | 4 | 1 | 0 | 2 |
subtype6 | 1 | 1 | 5 | 2 | 0 | 1 |
P value = 0.394 (Fisher's exact test), Q value = 0.53
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 12 | 30 | 32 |
subtype1 | 0 | 2 | 3 |
subtype2 | 2 | 5 | 5 |
subtype3 | 3 | 5 | 8 |
subtype4 | 5 | 8 | 3 |
subtype5 | 1 | 8 | 6 |
subtype6 | 1 | 2 | 7 |
P value = 0.235 (Fisher's exact test), Q value = 0.36
nPatients | 0 | 1 |
---|---|---|
ALL | 48 | 4 |
subtype1 | 4 | 1 |
subtype2 | 5 | 0 |
subtype3 | 13 | 0 |
subtype4 | 11 | 0 |
subtype5 | 9 | 2 |
subtype6 | 6 | 1 |
P value = 0.381 (Fisher's exact test), Q value = 0.52
nPatients | FEMALE | MALE |
---|---|---|
ALL | 32 | 42 |
subtype1 | 4 | 1 |
subtype2 | 5 | 7 |
subtype3 | 6 | 10 |
subtype4 | 8 | 8 |
subtype5 | 7 | 8 |
subtype6 | 2 | 8 |
P value = 0.677 (Fisher's exact test), Q value = 0.79
nPatients | NO | YES |
---|---|---|
ALL | 70 | 3 |
subtype1 | 4 | 0 |
subtype2 | 11 | 1 |
subtype3 | 16 | 0 |
subtype4 | 15 | 1 |
subtype5 | 15 | 0 |
subtype6 | 9 | 1 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/UVM-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UVM-TP/19775655/UVM-TP.merged_data.txt
-
Number of patients = 80
-
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 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.