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, 2 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 do not correlate to any clinical features.
-
4 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 5 subtypes that correlate to 'YEARS_TO_BIRTH'.
-
Consensus hierarchical clustering analysis on RPPA data identified 7 subtypes that do not correlate to any clinical features.
-
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'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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4 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 |
0.513 (0.981) |
0.691 (0.981) |
0.691 (0.981) |
0.858 (0.981) |
0.734 (0.981) |
METHLYATION CNMF |
0.193 (0.796) |
0.23 (0.796) |
0.914 (0.981) |
0.428 (0.981) |
0.516 (0.981) |
RPPA CNMF subtypes |
0.659 (0.981) |
0.00889 (0.222) |
0.99 (0.99) |
0.352 (0.981) |
0.427 (0.981) |
RPPA cHierClus subtypes |
0.543 (0.981) |
0.0513 (0.641) |
0.983 (0.99) |
0.403 (0.981) |
0.163 (0.796) |
RNAseq CNMF subtypes |
0.793 (0.981) |
0.345 (0.981) |
0.982 (0.99) |
0.217 (0.796) |
0.449 (0.981) |
RNAseq cHierClus subtypes |
0.0961 (0.796) |
0.234 (0.796) |
0.865 (0.981) |
0.00021 (0.0105) |
0.846 (0.981) |
MIRSEQ CNMF |
0.534 (0.981) |
0.0448 (0.641) |
0.635 (0.981) |
0.0854 (0.796) |
0.475 (0.981) |
MIRSEQ CHIERARCHICAL |
0.922 (0.981) |
0.209 (0.796) |
0.888 (0.981) |
0.839 (0.981) |
0.81 (0.981) |
MIRseq Mature CNMF subtypes |
0.638 (0.981) |
0.177 (0.796) |
0.616 (0.981) |
0.148 (0.796) |
0.813 (0.981) |
MIRseq Mature cHierClus subtypes |
0.83 (0.981) |
0.239 (0.796) |
0.836 (0.981) |
0.791 (0.981) |
0.8 (0.981) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 22 | 13 |
P value = 0.513 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (20.1) |
subtype1 | 21 | 13 | 6.7 - 140.3 (26.7) |
subtype2 | 22 | 14 | 2.7 - 80.8 (18.7) |
subtype3 | 12 | 7 | 0.3 - 88.1 (19.1) |
P value = 0.691 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 21 | 69.0 (7.9) |
subtype2 | 22 | 71.3 (10.4) |
subtype3 | 13 | 68.7 (10.0) |
P value = 0.691 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 24 |
subtype1 | 9 | 10 |
subtype2 | 13 | 8 |
subtype3 | 7 | 6 |
P value = 0.858 (Fisher's exact test), Q value = 0.98
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 19 | 13 |
subtype1 | 9 | 6 | 6 |
subtype2 | 10 | 7 | 5 |
subtype3 | 5 | 6 | 2 |
P value = 0.734 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 1 | 5 | 14 |
subtype2 | 1 | 3 | 18 |
subtype3 | 1 | 1 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 20 | 13 | 13 | 11 |
P value = 0.193 (logrank test), Q value = 0.8
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (21.0) |
subtype1 | 20 | 15 | 0.3 - 102.4 (20.7) |
subtype2 | 13 | 10 | 3.8 - 59.4 (19.9) |
subtype3 | 12 | 4 | 2.7 - 140.3 (23.8) |
subtype4 | 11 | 6 | 9.8 - 88.1 (23.5) |
P value = 0.23 (Kruskal-Wallis (anova)), Q value = 0.8
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 20 | 66.8 (7.7) |
subtype2 | 13 | 71.7 (10.9) |
subtype3 | 13 | 69.0 (8.4) |
subtype4 | 11 | 73.6 (10.0) |
P value = 0.914 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 9 | 9 |
subtype2 | 7 | 6 |
subtype3 | 6 | 6 |
subtype4 | 7 | 4 |
P value = 0.428 (Fisher's exact test), Q value = 0.98
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 24 | 20 | 13 |
subtype1 | 6 | 10 | 4 |
subtype2 | 4 | 5 | 4 |
subtype3 | 8 | 2 | 3 |
subtype4 | 6 | 3 | 2 |
P value = 0.516 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 4 | 16 |
subtype2 | 1 | 3 | 9 |
subtype3 | 1 | 2 | 10 |
subtype4 | 1 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 12 | 9 | 12 | 6 | 9 |
P value = 0.659 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 31 | 0.3 - 140.3 (21.9) |
subtype1 | 12 | 8 | 0.3 - 102.4 (27.1) |
subtype2 | 9 | 7 | 4.7 - 67.1 (12.4) |
subtype3 | 12 | 6 | 3.7 - 55.0 (23.0) |
subtype4 | 5 | 3 | 2.7 - 81.7 (6.7) |
subtype5 | 9 | 7 | 10.4 - 140.3 (25.4) |
P value = 0.00889 (Kruskal-Wallis (anova)), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 70.6 (9.0) |
subtype1 | 12 | 65.4 (8.1) |
subtype2 | 9 | 69.4 (6.8) |
subtype3 | 12 | 76.6 (9.3) |
subtype4 | 6 | 66.7 (9.7) |
subtype5 | 9 | 73.3 (6.7) |
P value = 0.99 (Fisher's exact test), Q value = 0.99
nPatients | NO | YES |
---|---|---|
ALL | 25 | 20 |
subtype1 | 6 | 5 |
subtype2 | 4 | 4 |
subtype3 | 6 | 5 |
subtype4 | 4 | 2 |
subtype5 | 5 | 4 |
P value = 0.352 (Fisher's exact test), Q value = 0.98
nPatients | UTERINE CARCINOSARCOMA/ MALIGNANT MIXED MULLERIAN TUMOR (MMMT): NOS | UTERINE CARCINOSARCOMA/ MMMT: HETEROLOGOUS TYPE | UTERINE CARCINOSARCOMA/MMMT: HOMOLOGOUS TYPE |
---|---|---|---|
ALL | 18 | 19 | 11 |
subtype1 | 5 | 6 | 1 |
subtype2 | 1 | 4 | 4 |
subtype3 | 6 | 2 | 4 |
subtype4 | 2 | 3 | 1 |
subtype5 | 4 | 4 | 1 |
P value = 0.427 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 36 |
subtype1 | 0 | 1 | 11 |
subtype2 | 0 | 1 | 8 |
subtype3 | 2 | 3 | 7 |
subtype4 | 1 | 1 | 4 |
subtype5 | 0 | 3 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 9 | 8 | 7 | 7 | 7 | 5 | 5 |
P value = 0.543 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 31 | 0.3 - 140.3 (21.9) |
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 - 27.2 (9.6) |
subtype7 | 5 | 4 | 10.4 - 140.3 (25.4) |
P value = 0.0513 (Kruskal-Wallis (anova)), Q value = 0.64
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 = 0.983 (Fisher's exact test), Q value = 0.99
nPatients | NO | YES |
---|---|---|
ALL | 25 | 20 |
subtype1 | 4 | 4 |
subtype2 | 4 | 3 |
subtype3 | 4 | 3 |
subtype4 | 5 | 2 |
subtype5 | 4 | 3 |
subtype6 | 2 | 2 |
subtype7 | 2 | 3 |
P value = 0.403 (Fisher's exact test), Q value = 0.98
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 = 0.8
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 | 16 | 19 | 12 | 10 |
P value = 0.793 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (21.0) |
subtype1 | 16 | 12 | 0.3 - 102.4 (22.7) |
subtype2 | 18 | 10 | 3.7 - 59.4 (23.6) |
subtype3 | 12 | 7 | 3.8 - 55.0 (16.5) |
subtype4 | 10 | 6 | 2.7 - 140.3 (36.3) |
P value = 0.345 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 69.7 (9.3) |
subtype1 | 16 | 69.5 (8.6) |
subtype2 | 19 | 72.1 (10.1) |
subtype3 | 12 | 69.2 (9.7) |
subtype4 | 10 | 66.2 (7.9) |
P value = 0.982 (Fisher's exact test), Q value = 0.99
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 7 | 7 |
subtype2 | 10 | 8 |
subtype3 | 7 | 5 |
subtype4 | 5 | 5 |
P value = 0.217 (Fisher's exact test), Q value = 0.8
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 | 9 | 2 |
subtype2 | 11 | 3 | 5 |
subtype3 | 5 | 5 | 2 |
subtype4 | 3 | 3 | 4 |
P value = 0.449 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 44 |
subtype1 | 0 | 3 | 13 |
subtype2 | 2 | 1 | 16 |
subtype3 | 1 | 2 | 8 |
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 = 0.0961 (logrank test), Q value = 0.8
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 56 | 35 | 0.3 - 140.3 (21.0) |
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 (22.6) |
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 (19.6) |
P value = 0.234 (Kruskal-Wallis (anova)), Q value = 0.8
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 = 0.865 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 25 |
subtype1 | 5 | 5 |
subtype2 | 1 | 2 |
subtype3 | 4 | 4 |
subtype4 | 5 | 1 |
subtype5 | 4 | 4 |
subtype6 | 3 | 3 |
subtype7 | 7 | 6 |
P value = 0.00021 (Fisher's exact test), Q value = 0.01
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 = 0.846 (Fisher's exact test), Q value = 0.98
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 |
---|---|---|---|
Number of samples | 15 | 24 | 17 |
P value = 0.534 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (20.1) |
subtype1 | 15 | 10 | 2.7 - 102.4 (17.2) |
subtype2 | 24 | 15 | 0.3 - 140.3 (26.7) |
subtype3 | 16 | 9 | 3.7 - 81.7 (23.6) |
P value = 0.0448 (Kruskal-Wallis (anova)), Q value = 0.64
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 15 | 67.9 (9.2) |
subtype2 | 24 | 68.0 (9.1) |
subtype3 | 17 | 74.1 (8.8) |
P value = 0.635 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 24 |
subtype1 | 8 | 5 |
subtype2 | 14 | 10 |
subtype3 | 7 | 9 |
P value = 0.0854 (Fisher's exact test), Q value = 0.8
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 | 9 | 2 |
subtype2 | 10 | 8 | 6 |
subtype3 | 10 | 2 | 5 |
P value = 0.475 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 3 | 12 |
subtype2 | 1 | 5 | 17 |
subtype3 | 2 | 1 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 24 | 8 | 18 | 6 |
P value = 0.922 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (20.1) |
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 | 15.8 - 27.2 (22.4) |
P value = 0.209 (Kruskal-Wallis (anova)), Q value = 0.8
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 = 0.888 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 24 |
subtype1 | 11 | 11 |
subtype2 | 4 | 4 |
subtype3 | 11 | 7 |
subtype4 | 3 | 2 |
P value = 0.839 (Fisher's exact test), Q value = 0.98
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 = 0.81 (Fisher's exact test), Q value = 0.98
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 | 4 |
---|---|---|---|---|
Number of samples | 10 | 14 | 14 | 18 |
P value = 0.638 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (20.1) |
subtype1 | 10 | 8 | 0.3 - 102.4 (23.2) |
subtype2 | 14 | 7 | 2.7 - 81.7 (21.3) |
subtype3 | 14 | 8 | 4.9 - 140.3 (25.1) |
subtype4 | 17 | 11 | 3.7 - 31.2 (19.6) |
P value = 0.177 (Kruskal-Wallis (anova)), Q value = 0.8
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 69.8 (9.3) |
subtype1 | 10 | 67.5 (8.5) |
subtype2 | 14 | 68.9 (8.2) |
subtype3 | 14 | 68.2 (10.0) |
subtype4 | 18 | 73.1 (9.9) |
P value = 0.616 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 24 |
subtype1 | 5 | 4 |
subtype2 | 5 | 8 |
subtype3 | 9 | 5 |
subtype4 | 10 | 7 |
P value = 0.148 (Fisher's exact test), Q value = 0.8
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 | 6 | 0 |
subtype2 | 4 | 5 | 5 |
subtype3 | 5 | 4 | 5 |
subtype4 | 11 | 4 | 3 |
P value = 0.813 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 9 | 43 |
subtype1 | 0 | 1 | 9 |
subtype2 | 0 | 3 | 11 |
subtype3 | 1 | 3 | 9 |
subtype4 | 2 | 2 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 25 | 7 | 17 | 7 |
P value = 0.83 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 34 | 0.3 - 140.3 (20.1) |
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 | 15.8 - 27.2 (25.2) |
P value = 0.239 (Kruskal-Wallis (anova)), Q value = 0.8
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 = 0.836 (Fisher's exact test), Q value = 0.98
nPatients | NO | YES |
---|---|---|
ALL | 29 | 24 |
subtype1 | 12 | 11 |
subtype2 | 3 | 4 |
subtype3 | 10 | 7 |
subtype4 | 4 | 2 |
P value = 0.791 (Fisher's exact test), Q value = 0.98
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 = 0.8 (Fisher's exact test), Q value = 0.98
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/22541488/UCS-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/22507158/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.