This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 5 clinical features across 57 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
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3 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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5 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 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 7 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 do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 7 subtypes that correlate to 'HISTOLOGICAL_TYPE'.
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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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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.168 (0.746) |
0.637 (1.00) |
0.487 (1.00) |
0.298 (0.876) |
0.536 (1.00) |
METHLYATION CNMF |
0.963 (1.00) |
0.102 (0.746) |
0.617 (1.00) |
0.154 (0.746) |
0.956 (1.00) |
RPPA CNMF subtypes |
0.938 (1.00) |
0.203 (0.746) |
0.813 (1.00) |
0.433 (1.00) |
0.51 (1.00) |
RPPA cHierClus subtypes |
0.384 (1.00) |
0.0513 (0.746) |
0.972 (1.00) |
0.403 (1.00) |
0.163 (0.746) |
RNAseq CNMF subtypes |
0.921 (1.00) |
0.205 (0.746) |
0.981 (1.00) |
0.166 (0.746) |
0.658 (1.00) |
RNAseq cHierClus subtypes |
0.0962 (0.746) |
0.234 (0.746) |
0.848 (1.00) |
0.00032 (0.016) |
0.845 (1.00) |
MIRSEQ CNMF |
0.141 (0.746) |
0.496 (1.00) |
0.625 (1.00) |
0.653 (1.00) |
0.829 (1.00) |
MIRSEQ CHIERARCHICAL |
0.929 (1.00) |
0.209 (0.746) |
0.875 (1.00) |
0.84 (1.00) |
0.814 (1.00) |
MIRseq Mature CNMF subtypes |
0.452 (1.00) |
0.0186 (0.465) |
1 (1.00) |
0.132 (0.746) |
0.713 (1.00) |
MIRseq Mature cHierClus subtypes |
0.818 (1.00) |
0.239 (0.746) |
0.915 (1.00) |
0.793 (1.00) |
0.803 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 21 | 17 |
P value = 0.168 (logrank test), Q value = 0.75
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (19.9) |
subtype1 | 18 | 10 | 6.7 - 140.3 (28.3) |
subtype2 | 21 | 12 | 2.7 - 67.1 (17.8) |
subtype3 | 16 | 12 | 0.3 - 88.1 (17.3) |
P value = 0.637 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 18 | 69.0 (8.3) |
subtype2 | 21 | 71.0 (9.7) |
subtype3 | 17 | 69.1 (10.3) |
P value = 0.487 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 7 | 10 |
subtype2 | 12 | 8 |
subtype3 | 10 | 7 |
P value = 0.298 (Fisher's exact test), Q value = 0.88
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 8 | 5 | 5 |
subtype2 | 8 | 6 | 7 |
subtype3 | 8 | 8 | 1 |
P value = 0.536 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 5 | 11 |
subtype2 | 1 | 2 | 18 |
subtype3 | 1 | 2 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 12 | 9 | 10 | 13 | 13 |
P value = 0.963 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (20.0) |
subtype1 | 12 | 8 | 0.3 - 102.4 (27.1) |
subtype2 | 9 | 6 | 4.7 - 81.7 (22.5) |
subtype3 | 10 | 7 | 5.5 - 59.4 (21.5) |
subtype4 | 12 | 6 | 2.7 - 140.3 (16.5) |
subtype5 | 13 | 8 | 3.8 - 88.1 (19.6) |
P value = 0.102 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 12 | 67.2 (8.0) |
subtype2 | 9 | 64.6 (6.7) |
subtype3 | 10 | 75.2 (9.2) |
subtype4 | 13 | 68.8 (9.6) |
subtype5 | 13 | 72.2 (9.8) |
P value = 0.617 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 26 |
subtype1 | 6 | 5 |
subtype2 | 3 | 5 |
subtype3 | 4 | 6 |
subtype4 | 7 | 6 |
subtype5 | 9 | 4 |
P value = 0.154 (Fisher's exact test), Q value = 0.75
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 20 | 13 |
subtype1 | 5 | 6 | 1 |
subtype2 | 1 | 4 | 4 |
subtype3 | 3 | 3 | 4 |
subtype4 | 9 | 2 | 2 |
subtype5 | 6 | 5 | 2 |
P value = 0.956 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 2 | 10 |
subtype2 | 0 | 1 | 8 |
subtype3 | 1 | 2 | 7 |
subtype4 | 1 | 3 | 9 |
subtype5 | 1 | 1 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 10 | 12 | 15 | 11 |
P value = 0.938 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 31 | 0.3 - 140.3 (20.1) |
subtype1 | 10 | 7 | 0.3 - 102.4 (22.4) |
subtype2 | 11 | 9 | 10.4 - 140.3 (25.4) |
subtype3 | 15 | 9 | 2.7 - 81.7 (13.7) |
subtype4 | 11 | 6 | 3.7 - 27.2 (19.6) |
P value = 0.203 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 70.6 (9.0) |
subtype1 | 10 | 67.9 (9.6) |
subtype2 | 12 | 70.0 (8.5) |
subtype3 | 15 | 69.6 (8.6) |
subtype4 | 11 | 75.1 (9.1) |
P value = 0.813 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 25 | 21 |
subtype1 | 5 | 5 |
subtype2 | 8 | 4 |
subtype3 | 6 | 7 |
subtype4 | 6 | 5 |
P value = 0.433 (Fisher's exact test), Q value = 1
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 18 | 19 | 11 |
subtype1 | 4 | 5 | 1 |
subtype2 | 5 | 6 | 1 |
subtype3 | 4 | 6 | 5 |
subtype4 | 5 | 2 | 4 |
P value = 0.51 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 36 |
subtype1 | 0 | 0 | 10 |
subtype2 | 1 | 3 | 8 |
subtype3 | 1 | 3 | 11 |
subtype4 | 1 | 3 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 9 | 8 | 7 | 7 | 7 | 5 | 5 |
P value = 0.384 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 31 | 0.3 - 140.3 (20.1) |
subtype1 | 9 | 6 | 0.3 - 102.4 (27.6) |
subtype2 | 7 | 5 | 2.7 - 81.7 (6.7) |
subtype3 | 7 | 4 | 12.2 - 80.8 (18.1) |
subtype4 | 7 | 5 | 4.9 - 67.1 (20.1) |
subtype5 | 7 | 4 | 19.6 - 29.9 (23.5) |
subtype6 | 5 | 3 | 3.7 - 22.9 (9.6) |
subtype7 | 5 | 4 | 10.4 - 140.3 (25.4) |
P value = 0.0513 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 70.6 (9.0) |
subtype1 | 9 | 68.1 (8.7) |
subtype2 | 8 | 65.8 (6.8) |
subtype3 | 7 | 66.1 (8.1) |
subtype4 | 7 | 73.3 (9.8) |
subtype5 | 7 | 73.3 (9.6) |
subtype6 | 5 | 81.2 (7.4) |
subtype7 | 5 | 71.0 (4.9) |
P value = 0.972 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 25 | 21 |
subtype1 | 4 | 4 |
subtype2 | 4 | 3 |
subtype3 | 4 | 3 |
subtype4 | 5 | 2 |
subtype5 | 4 | 3 |
subtype6 | 2 | 3 |
subtype7 | 2 | 3 |
P value = 0.403 (Fisher's exact test), Q value = 1
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 18 | 19 | 11 |
subtype1 | 4 | 4 | 1 |
subtype2 | 2 | 4 | 2 |
subtype3 | 3 | 4 | 0 |
subtype4 | 1 | 3 | 3 |
subtype5 | 2 | 2 | 3 |
subtype6 | 3 | 0 | 2 |
subtype7 | 3 | 2 | 0 |
P value = 0.163 (Fisher's exact test), Q value = 0.75
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 36 |
subtype1 | 0 | 2 | 7 |
subtype2 | 1 | 2 | 5 |
subtype3 | 0 | 0 | 7 |
subtype4 | 0 | 0 | 7 |
subtype5 | 1 | 3 | 3 |
subtype6 | 1 | 0 | 4 |
subtype7 | 0 | 2 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 15 | 20 | 12 | 10 |
P value = 0.921 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (20.0) |
subtype1 | 15 | 11 | 0.3 - 102.4 (20.1) |
subtype2 | 19 | 10 | 3.7 - 59.4 (19.9) |
subtype3 | 12 | 8 | 3.8 - 88.1 (16.5) |
subtype4 | 10 | 6 | 2.7 - 140.3 (23.9) |
P value = 0.205 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 15 | 69.8 (8.9) |
subtype2 | 20 | 71.9 (9.9) |
subtype3 | 12 | 70.2 (10.2) |
subtype4 | 10 | 64.7 (6.3) |
P value = 0.981 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 26 |
subtype1 | 7 | 6 |
subtype2 | 10 | 10 |
subtype3 | 7 | 5 |
subtype4 | 5 | 5 |
P value = 0.166 (Fisher's exact test), Q value = 0.75
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 20 | 13 |
subtype1 | 5 | 8 | 2 |
subtype2 | 12 | 3 | 5 |
subtype3 | 5 | 5 | 2 |
subtype4 | 2 | 4 | 4 |
P value = 0.658 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 3 | 12 |
subtype2 | 2 | 2 | 16 |
subtype3 | 1 | 1 | 9 |
subtype4 | 0 | 3 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 11 | 4 | 8 | 6 | 8 | 6 | 14 |
P value = 0.0962 (logrank test), Q value = 0.75
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (20.0) |
subtype1 | 11 | 7 | 0.3 - 102.4 (27.6) |
subtype2 | 4 | 4 | 4.7 - 22.5 (9.0) |
subtype3 | 8 | 4 | 11.9 - 59.4 (21.5) |
subtype4 | 6 | 5 | 3.8 - 88.1 (14.8) |
subtype5 | 8 | 4 | 2.7 - 81.7 (30.0) |
subtype6 | 6 | 3 | 9.8 - 55.0 (26.7) |
subtype7 | 13 | 8 | 3.7 - 140.3 (19.3) |
P value = 0.234 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 11 | 67.4 (8.0) |
subtype2 | 4 | 71.2 (4.3) |
subtype3 | 8 | 74.6 (8.1) |
subtype4 | 6 | 66.8 (8.4) |
subtype5 | 8 | 64.6 (6.8) |
subtype6 | 6 | 73.0 (11.9) |
subtype7 | 14 | 71.1 (11.2) |
P value = 0.848 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 26 |
subtype1 | 5 | 5 |
subtype2 | 1 | 2 |
subtype3 | 4 | 4 |
subtype4 | 5 | 1 |
subtype5 | 4 | 4 |
subtype6 | 3 | 3 |
subtype7 | 7 | 7 |
P value = 0.00032 (Fisher's exact test), Q value = 0.016
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 20 | 13 |
subtype1 | 5 | 5 | 1 |
subtype2 | 0 | 3 | 1 |
subtype3 | 1 | 2 | 5 |
subtype4 | 1 | 5 | 0 |
subtype5 | 1 | 3 | 4 |
subtype6 | 4 | 1 | 1 |
subtype7 | 12 | 1 | 1 |
P value = 0.845 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 3 | 8 |
subtype2 | 0 | 1 | 3 |
subtype3 | 1 | 2 | 5 |
subtype4 | 0 | 0 | 5 |
subtype5 | 0 | 1 | 7 |
subtype6 | 1 | 0 | 5 |
subtype7 | 1 | 2 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 11 | 22 | 4 | 19 |
P value = 0.141 (logrank test), Q value = 0.75
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (19.9) |
subtype1 | 11 | 8 | 4.7 - 102.4 (18.8) |
subtype2 | 22 | 13 | 0.3 - 140.3 (26.7) |
subtype3 | 4 | 1 | 2.7 - 81.7 (40.9) |
subtype4 | 18 | 12 | 3.7 - 31.2 (17.5) |
P value = 0.496 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 11 | 69.4 (8.8) |
subtype2 | 22 | 68.5 (9.3) |
subtype3 | 4 | 67.5 (7.5) |
subtype4 | 19 | 72.0 (10.2) |
P value = 0.625 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 4 | 5 |
subtype2 | 13 | 9 |
subtype3 | 1 | 3 |
subtype4 | 11 | 8 |
P value = 0.653 (Fisher's exact test), Q value = 1
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 4 | 5 | 2 |
subtype2 | 8 | 8 | 6 |
subtype3 | 1 | 1 | 2 |
subtype4 | 11 | 5 | 3 |
P value = 0.829 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 2 | 9 |
subtype2 | 1 | 5 | 15 |
subtype3 | 0 | 0 | 4 |
subtype4 | 2 | 2 | 15 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 8 | 18 | 6 |
P value = 0.929 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (19.9) |
subtype1 | 23 | 14 | 2.7 - 102.4 (18.8) |
subtype2 | 8 | 6 | 0.3 - 80.8 (27.1) |
subtype3 | 18 | 11 | 3.8 - 140.3 (25.0) |
subtype4 | 6 | 3 | 13.4 - 25.7 (18.7) |
P value = 0.209 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 24 | 70.9 (9.8) |
subtype2 | 8 | 67.4 (8.7) |
subtype3 | 18 | 67.7 (9.1) |
subtype4 | 6 | 74.8 (8.0) |
P value = 0.875 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 11 | 11 |
subtype2 | 4 | 4 |
subtype3 | 11 | 7 |
subtype4 | 3 | 3 |
P value = 0.84 (Fisher's exact test), Q value = 1
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 12 | 8 | 4 |
subtype2 | 4 | 3 | 1 |
subtype3 | 6 | 6 | 6 |
subtype4 | 2 | 2 | 2 |
P value = 0.814 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 3 | 20 |
subtype2 | 0 | 2 | 6 |
subtype3 | 1 | 3 | 13 |
subtype4 | 1 | 1 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 23 | 20 |
P value = 0.452 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (19.9) |
subtype1 | 13 | 8 | 2.7 - 102.4 (14.7) |
subtype2 | 23 | 14 | 0.3 - 140.3 (27.6) |
subtype3 | 19 | 12 | 3.7 - 51.8 (19.6) |
P value = 0.0186 (Kruskal-Wallis (anova)), Q value = 0.46
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 13 | 66.7 (6.2) |
subtype2 | 23 | 67.9 (9.2) |
subtype3 | 20 | 74.0 (10.0) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 6 | 5 |
subtype2 | 12 | 11 |
subtype3 | 11 | 9 |
P value = 0.132 (Fisher's exact test), Q value = 0.75
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 3 | 8 | 2 |
subtype2 | 9 | 7 | 7 |
subtype3 | 12 | 4 | 4 |
P value = 0.713 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 2 | 11 |
subtype2 | 1 | 5 | 16 |
subtype3 | 2 | 2 | 16 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 25 | 7 | 17 | 7 |
P value = 0.818 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (19.9) |
subtype1 | 24 | 15 | 2.7 - 102.4 (18.4) |
subtype2 | 7 | 5 | 0.3 - 80.8 (27.6) |
subtype3 | 17 | 10 | 4.9 - 140.3 (23.5) |
subtype4 | 7 | 4 | 13.4 - 26.6 (19.6) |
P value = 0.239 (Kruskal-Wallis (anova)), Q value = 0.75
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 25 | 70.6 (9.8) |
subtype2 | 7 | 67.4 (9.4) |
subtype3 | 17 | 67.8 (9.3) |
subtype4 | 7 | 74.3 (7.4) |
P value = 0.915 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 12 | 11 |
subtype2 | 3 | 4 |
subtype3 | 10 | 7 |
subtype4 | 4 | 3 |
P value = 0.793 (Fisher's exact test), Q value = 1
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/ MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 12 | 9 | 4 |
subtype2 | 4 | 2 | 1 |
subtype3 | 6 | 5 | 6 |
subtype4 | 2 | 3 | 2 |
P value = 0.803 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 3 | 21 |
subtype2 | 0 | 1 | 6 |
subtype3 | 1 | 4 | 11 |
subtype4 | 1 | 1 | 5 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/20140950/UCS-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/19775681/UCS-TP.merged_data.txt
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Number of patients = 57
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Number of clustering approaches = 10
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Number of selected clinical features = 5
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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.