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 7 clinical features across 47 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
2 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 2 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 2 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
5 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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8 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'ETHNICITY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE | ETHNICITY |
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 |
0.401 (0.802) |
0.554 (0.873) |
0.245 (0.636) |
0.22 (0.636) |
0.2 (0.636) |
0.423 (0.822) |
1 (1.00) |
METHLYATION CNMF |
0.235 (0.636) |
0.307 (0.693) |
0.561 (0.873) |
0.0984 (0.636) |
0.192 (0.636) |
0.0997 (0.636) |
0.74 (1.00) |
RPPA CNMF subtypes |
0.0873 (0.636) |
0.97 (1.00) |
1 (1.00) |
0.654 (0.954) |
1 (1.00) |
1 (1.00) |
0.209 (0.636) |
RPPA cHierClus subtypes |
0.306 (0.693) |
0.616 (0.937) |
1 (1.00) |
0.823 (1.00) |
0.479 (0.869) |
0.243 (0.636) |
1 (1.00) |
RNAseq CNMF subtypes |
0.161 (0.636) |
0.153 (0.636) |
0.151 (0.636) |
1 (1.00) |
0.485 (0.869) |
0.124 (0.636) |
1 (1.00) |
RNAseq cHierClus subtypes |
0.0923 (0.636) |
0.547 (0.873) |
0.293 (0.693) |
1 (1.00) |
0.632 (0.942) |
0.522 (0.869) |
1 (1.00) |
MIRSEQ CNMF |
0.972 (1.00) |
0.947 (1.00) |
0.194 (0.636) |
0.155 (0.636) |
0.0593 (0.636) |
0.864 (1.00) |
0.274 (0.686) |
MIRSEQ CHIERARCHICAL |
0.511 (0.869) |
0.882 (1.00) |
0.185 (0.636) |
0.152 (0.636) |
0.0273 (0.636) |
0.977 (1.00) |
0.0167 (0.583) |
MIRseq Mature CNMF subtypes |
0.949 (1.00) |
0.511 (0.869) |
0.355 (0.753) |
0.373 (0.767) |
0.0368 (0.636) |
0.333 (0.728) |
0.724 (1.00) |
MIRseq Mature cHierClus subtypes |
0.936 (1.00) |
0.754 (1.00) |
0.47 (0.869) |
0.201 (0.636) |
0.239 (0.636) |
0.118 (0.636) |
0.00209 (0.146) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 29 | 18 |
P value = 0.401 (logrank test), Q value = 0.8
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 29 | 7 | 0.0 - 211.2 (25.1) |
subtype2 | 18 | 2 | 0.6 - 196.6 (31.4) |
P value = 0.554 (Wilcoxon-test), Q value = 0.87
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 56.3 (14.1) |
subtype1 | 29 | 55.0 (14.9) |
subtype2 | 18 | 58.3 (12.9) |
P value = 0.245 (Fisher's exact test), Q value = 0.64
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 21 |
subtype1 | 14 | 15 |
subtype2 | 12 | 6 |
P value = 0.22 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 39 | 7 |
subtype1 | 22 | 6 |
subtype2 | 17 | 1 |
P value = 0.2 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 40 | 3 | 4 |
subtype1 | 24 | 1 | 4 |
subtype2 | 16 | 2 | 0 |
P value = 0.423 (Fisher's exact test), Q value = 0.82
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 28 |
subtype1 | 9 | 1 | 19 |
subtype2 | 9 | 0 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 35 |
subtype1 | 7 | 22 |
subtype2 | 5 | 13 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 24 | 23 |
P value = 0.235 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 24 | 3 | 1.9 - 196.6 (41.9) |
subtype2 | 23 | 6 | 0.0 - 211.2 (25.9) |
P value = 0.307 (Wilcoxon-test), Q value = 0.69
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 56.3 (14.1) |
subtype1 | 24 | 54.2 (15.0) |
subtype2 | 23 | 58.5 (13.1) |
P value = 0.561 (Fisher's exact test), Q value = 0.87
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 21 |
subtype1 | 12 | 12 |
subtype2 | 14 | 9 |
P value = 0.0984 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 39 | 7 |
subtype1 | 18 | 6 |
subtype2 | 21 | 1 |
P value = 0.192 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 40 | 3 | 4 |
subtype1 | 21 | 0 | 3 |
subtype2 | 19 | 3 | 1 |
P value = 0.0997 (Fisher's exact test), Q value = 0.64
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 28 |
subtype1 | 6 | 1 | 17 |
subtype2 | 12 | 0 | 11 |
P value = 0.74 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 35 |
subtype1 | 7 | 17 |
subtype2 | 5 | 18 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 17 | 15 |
P value = 0.0873 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 6 | 0.0 - 211.2 (24.7) |
subtype1 | 17 | 2 | 0.0 - 211.2 (31.1) |
subtype2 | 15 | 4 | 1.9 - 70.1 (22.3) |
P value = 0.97 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 54.8 (14.4) |
subtype1 | 17 | 54.7 (15.3) |
subtype2 | 15 | 54.9 (13.8) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 17 |
subtype1 | 8 | 9 |
subtype2 | 7 | 8 |
P value = 0.654 (Fisher's exact test), Q value = 0.95
nPatients | NO | YES |
---|---|---|
ALL | 26 | 5 |
subtype1 | 14 | 2 |
subtype2 | 12 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 26 | 2 | 4 |
subtype1 | 14 | 1 | 2 |
subtype2 | 12 | 1 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 16 |
subtype1 | 9 | 8 |
subtype2 | 7 | 8 |
P value = 0.209 (Fisher's exact test), Q value = 0.64
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 25 |
subtype1 | 2 | 15 |
subtype2 | 5 | 10 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 14 | 12 |
P value = 0.306 (logrank test), Q value = 0.69
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 6 | 0.0 - 211.2 (24.7) |
subtype1 | 6 | 1 | 0.0 - 70.1 (8.6) |
subtype2 | 14 | 2 | 12.7 - 211.2 (31.4) |
subtype3 | 12 | 3 | 1.9 - 196.6 (23.2) |
P value = 0.616 (Kruskal-Wallis (anova)), Q value = 0.94
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 32 | 54.8 (14.4) |
subtype1 | 6 | 55.2 (16.9) |
subtype2 | 14 | 52.1 (15.3) |
subtype3 | 12 | 57.8 (12.6) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 17 |
subtype1 | 3 | 3 |
subtype2 | 6 | 8 |
subtype3 | 6 | 6 |
P value = 0.823 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 26 | 5 |
subtype1 | 5 | 0 |
subtype2 | 11 | 3 |
subtype3 | 10 | 2 |
P value = 0.479 (Fisher's exact test), Q value = 0.87
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 26 | 2 | 4 |
subtype1 | 5 | 1 | 0 |
subtype2 | 11 | 0 | 3 |
subtype3 | 10 | 1 | 1 |
P value = 0.243 (Fisher's exact test), Q value = 0.64
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 16 |
subtype1 | 1 | 5 |
subtype2 | 8 | 6 |
subtype3 | 7 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 25 |
subtype1 | 1 | 5 |
subtype2 | 3 | 11 |
subtype3 | 3 | 9 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 15 | 13 |
P value = 0.161 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 28 | 6 | 0.0 - 211.2 (31.8) |
subtype1 | 15 | 3 | 0.0 - 211.2 (52.0) |
subtype2 | 13 | 3 | 1.9 - 98.1 (24.7) |
P value = 0.153 (Wilcoxon-test), Q value = 0.64
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 28 | 56.5 (12.3) |
subtype1 | 15 | 60.1 (9.9) |
subtype2 | 13 | 52.4 (13.7) |
P value = 0.151 (Fisher's exact test), Q value = 0.64
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 13 |
subtype1 | 6 | 9 |
subtype2 | 9 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 26 | 1 |
subtype1 | 13 | 1 |
subtype2 | 13 | 0 |
P value = 0.485 (Fisher's exact test), Q value = 0.87
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 25 | 2 | 1 |
subtype1 | 13 | 2 | 0 |
subtype2 | 12 | 0 | 1 |
P value = 0.124 (Fisher's exact test), Q value = 0.64
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 1 | 16 |
subtype1 | 4 | 0 | 11 |
subtype2 | 7 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 27 |
subtype1 | 1 | 14 |
subtype2 | 0 | 13 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 10 | 5 |
P value = 0.0923 (logrank test), Q value = 0.64
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 28 | 6 | 0.0 - 211.2 (31.8) |
subtype1 | 13 | 2 | 4.3 - 211.2 (35.5) |
subtype2 | 10 | 3 | 1.9 - 98.1 (24.7) |
subtype3 | 5 | 1 | 0.0 - 57.2 (42.7) |
P value = 0.547 (Kruskal-Wallis (anova)), Q value = 0.87
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 28 | 56.5 (12.3) |
subtype1 | 13 | 58.8 (12.7) |
subtype2 | 10 | 54.7 (13.0) |
subtype3 | 5 | 54.2 (10.9) |
P value = 0.293 (Fisher's exact test), Q value = 0.69
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 13 |
subtype1 | 5 | 8 |
subtype2 | 6 | 4 |
subtype3 | 4 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 26 | 1 |
subtype1 | 12 | 1 |
subtype2 | 10 | 0 |
subtype3 | 4 | 0 |
P value = 0.632 (Fisher's exact test), Q value = 0.94
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 25 | 2 | 1 |
subtype1 | 11 | 1 | 1 |
subtype2 | 10 | 0 | 0 |
subtype3 | 4 | 1 | 0 |
P value = 0.522 (Fisher's exact test), Q value = 0.87
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 11 | 1 | 16 |
subtype1 | 5 | 0 | 8 |
subtype2 | 5 | 1 | 4 |
subtype3 | 1 | 0 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 27 |
subtype1 | 1 | 12 |
subtype2 | 0 | 10 |
subtype3 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 13 | 11 | 10 | 12 |
P value = 0.972 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 46 | 9 | 0.0 - 211.2 (26.7) |
subtype1 | 13 | 3 | 0.0 - 211.2 (24.7) |
subtype2 | 11 | 2 | 1.9 - 111.6 (24.6) |
subtype3 | 10 | 2 | 9.8 - 128.1 (24.8) |
subtype4 | 12 | 2 | 4.1 - 116.8 (43.8) |
P value = 0.947 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 46 | 56.3 (14.3) |
subtype1 | 13 | 58.7 (9.2) |
subtype2 | 11 | 57.5 (12.1) |
subtype3 | 10 | 55.5 (16.3) |
subtype4 | 12 | 53.2 (19.2) |
P value = 0.194 (Fisher's exact test), Q value = 0.64
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 21 |
subtype1 | 6 | 7 |
subtype2 | 8 | 3 |
subtype3 | 3 | 7 |
subtype4 | 8 | 4 |
P value = 0.155 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 39 | 6 |
subtype1 | 12 | 0 |
subtype2 | 9 | 2 |
subtype3 | 7 | 3 |
subtype4 | 11 | 1 |
P value = 0.0593 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 39 | 3 | 4 |
subtype1 | 10 | 3 | 0 |
subtype2 | 9 | 0 | 2 |
subtype3 | 10 | 0 | 0 |
subtype4 | 10 | 0 | 2 |
P value = 0.864 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 27 |
subtype1 | 5 | 0 | 8 |
subtype2 | 4 | 1 | 6 |
subtype3 | 5 | 0 | 5 |
subtype4 | 4 | 0 | 8 |
P value = 0.274 (Fisher's exact test), Q value = 0.69
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 34 |
subtype1 | 2 | 11 |
subtype2 | 3 | 8 |
subtype3 | 5 | 5 |
subtype4 | 2 | 10 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 9 | 12 | 7 | 12 | 6 |
P value = 0.511 (logrank test), Q value = 0.87
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 46 | 9 | 0.0 - 211.2 (26.7) |
subtype1 | 9 | 1 | 4.3 - 211.2 (31.1) |
subtype2 | 12 | 3 | 1.9 - 116.8 (24.9) |
subtype3 | 7 | 2 | 0.0 - 196.6 (14.0) |
subtype4 | 12 | 2 | 9.8 - 128.1 (35.3) |
subtype5 | 6 | 1 | 4.1 - 98.1 (31.8) |
P value = 0.882 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 46 | 56.3 (14.3) |
subtype1 | 9 | 56.3 (10.4) |
subtype2 | 12 | 58.8 (12.6) |
subtype3 | 7 | 57.7 (9.8) |
subtype4 | 12 | 56.2 (18.9) |
subtype5 | 6 | 49.8 (18.3) |
P value = 0.185 (Fisher's exact test), Q value = 0.64
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 21 |
subtype1 | 2 | 7 |
subtype2 | 8 | 4 |
subtype3 | 4 | 3 |
subtype4 | 6 | 6 |
subtype5 | 5 | 1 |
P value = 0.152 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 39 | 6 |
subtype1 | 9 | 0 |
subtype2 | 10 | 2 |
subtype3 | 6 | 0 |
subtype4 | 8 | 4 |
subtype5 | 6 | 0 |
P value = 0.0273 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 39 | 3 | 4 |
subtype1 | 9 | 0 | 0 |
subtype2 | 10 | 0 | 2 |
subtype3 | 4 | 3 | 0 |
subtype4 | 11 | 0 | 1 |
subtype5 | 5 | 0 | 1 |
P value = 0.977 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 27 |
subtype1 | 4 | 0 | 5 |
subtype2 | 4 | 1 | 7 |
subtype3 | 3 | 0 | 4 |
subtype4 | 4 | 0 | 8 |
subtype5 | 3 | 0 | 3 |
P value = 0.0167 (Fisher's exact test), Q value = 0.58
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 34 |
subtype1 | 0 | 9 |
subtype2 | 3 | 9 |
subtype3 | 2 | 5 |
subtype4 | 7 | 5 |
subtype5 | 0 | 6 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 18 | 23 |
P value = 0.949 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 41 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 18 | 4 | 0.0 - 211.2 (24.2) |
subtype2 | 23 | 5 | 1.9 - 128.1 (41.2) |
P value = 0.511 (Wilcoxon-test), Q value = 0.87
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 41 | 55.1 (14.1) |
subtype1 | 18 | 56.9 (12.7) |
subtype2 | 23 | 53.7 (15.3) |
P value = 0.355 (Fisher's exact test), Q value = 0.75
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 19 |
subtype1 | 8 | 10 |
subtype2 | 14 | 9 |
P value = 0.373 (Fisher's exact test), Q value = 0.77
nPatients | NO | YES |
---|---|---|
ALL | 35 | 5 |
subtype1 | 16 | 1 |
subtype2 | 19 | 4 |
P value = 0.0368 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 35 | 3 | 3 |
subtype1 | 15 | 3 | 0 |
subtype2 | 20 | 0 | 3 |
P value = 0.333 (Fisher's exact test), Q value = 0.73
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 16 | 1 | 24 |
subtype1 | 9 | 0 | 9 |
subtype2 | 7 | 1 | 15 |
P value = 0.724 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 31 |
subtype1 | 5 | 13 |
subtype2 | 5 | 18 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|
Number of samples | 3 | 5 | 6 | 6 | 8 | 3 | 5 | 2 | 3 |
P value = 0.936 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 39 | 8 | 0.0 - 211.2 (26.0) |
subtype1 | 3 | 0 | 4.3 - 22.3 (14.0) |
subtype2 | 5 | 1 | 1.9 - 42.7 (18.2) |
subtype3 | 6 | 2 | 0.6 - 196.6 (24.6) |
subtype4 | 6 | 1 | 10.3 - 38.2 (24.8) |
subtype5 | 8 | 2 | 4.1 - 211.2 (29.2) |
subtype6 | 3 | 1 | 35.5 - 116.8 (52.0) |
subtype7 | 5 | 1 | 0.0 - 52.0 (32.0) |
subtype9 | 3 | 0 | 45.1 - 128.1 (111.6) |
P value = 0.754 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 39 | 55.5 (14.3) |
subtype1 | 3 | 61.0 (13.5) |
subtype2 | 5 | 58.0 (14.2) |
subtype3 | 6 | 47.2 (19.7) |
subtype4 | 6 | 62.0 (10.3) |
subtype5 | 8 | 51.6 (12.1) |
subtype6 | 3 | 54.7 (23.1) |
subtype7 | 5 | 60.0 (6.3) |
subtype9 | 3 | 53.0 (21.2) |
P value = 0.47 (Fisher's exact test), Q value = 0.87
nPatients | FEMALE | MALE |
---|---|---|
ALL | 21 | 18 |
subtype1 | 2 | 1 |
subtype2 | 3 | 2 |
subtype3 | 3 | 3 |
subtype4 | 2 | 4 |
subtype5 | 4 | 4 |
subtype6 | 1 | 2 |
subtype7 | 5 | 0 |
subtype9 | 1 | 2 |
P value = 0.201 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 33 | 5 |
subtype1 | 3 | 0 |
subtype2 | 4 | 1 |
subtype3 | 5 | 1 |
subtype4 | 5 | 1 |
subtype5 | 8 | 0 |
subtype6 | 3 | 0 |
subtype7 | 4 | 0 |
subtype9 | 1 | 2 |
P value = 0.239 (Fisher's exact test), Q value = 0.64
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 33 | 3 | 3 |
subtype1 | 3 | 0 | 0 |
subtype2 | 4 | 0 | 1 |
subtype3 | 3 | 2 | 1 |
subtype4 | 6 | 0 | 0 |
subtype5 | 8 | 0 | 0 |
subtype6 | 2 | 0 | 1 |
subtype7 | 4 | 1 | 0 |
subtype9 | 3 | 0 | 0 |
P value = 0.118 (Fisher's exact test), Q value = 0.64
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 23 |
subtype1 | 2 | 1 |
subtype2 | 1 | 4 |
subtype3 | 1 | 5 |
subtype4 | 4 | 2 |
subtype5 | 6 | 2 |
subtype6 | 1 | 2 |
subtype7 | 1 | 4 |
subtype9 | 0 | 3 |
P value = 0.00209 (Fisher's exact test), Q value = 0.15
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 29 |
subtype1 | 0 | 3 |
subtype2 | 1 | 4 |
subtype3 | 4 | 2 |
subtype4 | 2 | 4 |
subtype5 | 0 | 8 |
subtype6 | 0 | 3 |
subtype7 | 0 | 5 |
subtype9 | 3 | 0 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/20125263/DLBC-TP.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/19775131/DLBC-TP.merged_data.txt
-
Number of patients = 47
-
Number of clustering approaches = 10
-
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.