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 8 clinical features across 48 patients, no 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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4 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 6 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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5 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 |
TUMOR TISSUE SITE |
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 | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.515 (0.777) |
0.654 (0.894) |
0.428 (0.713) |
0.387 (0.709) |
1 (1.00) |
0.256 (0.571) |
0.0713 (0.408) |
0.59 (0.842) |
METHLYATION CNMF |
0.93 (1.00) |
0.654 (0.894) |
0.151 (0.483) |
0.975 (1.00) |
0.127 (0.46) |
0.0415 (0.332) |
0.257 (0.571) |
0.339 (0.66) |
RPPA CNMF subtypes |
0.346 (0.66) |
0.933 (1.00) |
0.457 (0.717) |
0.746 (0.947) |
0.322 (0.645) |
0.183 (0.523) |
0.19 (0.523) |
0.399 (0.709) |
RPPA cHierClus subtypes |
0.306 (0.628) |
0.572 (0.842) |
0.393 (0.709) |
0.902 (1.00) |
0.83 (1.00) |
0.427 (0.713) |
0.277 (0.599) |
1 (1.00) |
RNAseq CNMF subtypes |
0.917 (1.00) |
0.437 (0.713) |
0.0405 (0.332) |
0.446 (0.714) |
0.226 (0.547) |
0.0365 (0.332) |
0.21 (0.542) |
0.083 (0.415) |
RNAseq cHierClus subtypes |
0.302 (0.628) |
0.682 (0.897) |
0.0603 (0.402) |
0.974 (1.00) |
0.0886 (0.415) |
0.0795 (0.415) |
0.854 (1.00) |
0.209 (0.542) |
MIRSEQ CNMF |
0.684 (0.897) |
0.855 (1.00) |
0.103 (0.424) |
0.581 (0.842) |
0.0671 (0.408) |
0.233 (0.549) |
0.73 (0.942) |
0.0365 (0.332) |
MIRSEQ CHIERARCHICAL |
0.511 (0.777) |
0.888 (1.00) |
0.901 (1.00) |
0.171 (0.523) |
0.138 (0.481) |
0.0401 (0.332) |
0.982 (1.00) |
0.0177 (0.332) |
MIRseq Mature CNMF subtypes |
0.986 (1.00) |
0.798 (0.997) |
0.411 (0.713) |
0.186 (0.523) |
0.0398 (0.332) |
0.0197 (0.332) |
0.145 (0.483) |
0.0189 (0.332) |
MIRseq Mature cHierClus subtypes |
0.969 (1.00) |
0.223 (0.547) |
0.0472 (0.343) |
0.659 (0.894) |
0.0934 (0.415) |
0.125 (0.46) |
0.106 (0.424) |
0.0272 (0.332) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 20 | 7 | 21 |
P value = 0.515 (logrank test), Q value = 0.78
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 19 | 5 | 0.0 - 211.2 (32.0) |
subtype2 | 7 | 2 | 1.9 - 196.6 (24.0) |
subtype3 | 21 | 2 | 4.1 - 128.1 (27.4) |
P value = 0.654 (Kruskal-Wallis (anova)), Q value = 0.89
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 56.3 (13.9) |
subtype1 | 20 | 53.9 (14.7) |
subtype2 | 7 | 56.0 (14.2) |
subtype3 | 21 | 58.7 (13.4) |
P value = 0.428 (Fisher's exact test), Q value = 0.71
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 2 |
subtype1 | 1 | 1 | 2 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 2 | 2 |
subtype2 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 1 | 0 | 2 | 2 | 1 | 1 | 0 | 0 | 1 | 3 | 0 | 0 | 0 |
P value = 0.387 (Fisher's exact test), Q value = 0.71
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 22 |
subtype1 | 12 | 8 |
subtype2 | 2 | 5 |
subtype3 | 12 | 9 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 40 | 7 |
subtype1 | 16 | 3 |
subtype2 | 6 | 1 |
subtype3 | 18 | 3 |
P value = 0.256 (Fisher's exact test), Q value = 0.57
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 41 | 3 | 4 |
subtype1 | 15 | 2 | 3 |
subtype2 | 6 | 0 | 1 |
subtype3 | 20 | 1 | 0 |
P value = 0.0713 (Fisher's exact test), Q value = 0.41
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 29 |
subtype1 | 5 | 1 | 14 |
subtype2 | 1 | 0 | 6 |
subtype3 | 12 | 0 | 9 |
P value = 0.59 (Fisher's exact test), Q value = 0.84
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 36 |
subtype1 | 4 | 16 |
subtype2 | 1 | 6 |
subtype3 | 7 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 13 | 19 | 7 |
P value = 0.93 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 9 | 2 | 1.9 - 150.5 (35.5) |
subtype2 | 13 | 2 | 4.3 - 128.1 (41.2) |
subtype3 | 18 | 4 | 0.0 - 211.2 (23.5) |
subtype4 | 7 | 1 | 19.6 - 196.6 (31.7) |
P value = 0.654 (Kruskal-Wallis (anova)), Q value = 0.89
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 56.3 (13.9) |
subtype1 | 9 | 52.1 (19.2) |
subtype2 | 13 | 53.6 (15.4) |
subtype3 | 19 | 59.8 (11.3) |
subtype4 | 7 | 56.9 (9.5) |
P value = 0.151 (Fisher's exact test), Q value = 0.48
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 2 |
subtype1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 |
subtype2 | 0 | 2 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
subtype3 | 2 | 0 | 2 | 3 | 1 | 1 | 0 | 1 | 0 | 2 | 1 | 1 | 0 |
subtype4 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
P value = 0.975 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 22 |
subtype1 | 4 | 5 |
subtype2 | 7 | 6 |
subtype3 | 11 | 8 |
subtype4 | 4 | 3 |
P value = 0.127 (Fisher's exact test), Q value = 0.46
nPatients | NO | YES |
---|---|---|
ALL | 40 | 7 |
subtype1 | 6 | 3 |
subtype2 | 10 | 3 |
subtype3 | 17 | 1 |
subtype4 | 7 | 0 |
P value = 0.0415 (Fisher's exact test), Q value = 0.33
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 41 | 3 | 4 |
subtype1 | 6 | 0 | 3 |
subtype2 | 12 | 0 | 1 |
subtype3 | 16 | 3 | 0 |
subtype4 | 7 | 0 | 0 |
P value = 0.257 (Fisher's exact test), Q value = 0.57
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 29 |
subtype1 | 3 | 0 | 6 |
subtype2 | 2 | 1 | 10 |
subtype3 | 9 | 0 | 10 |
subtype4 | 4 | 0 | 3 |
P value = 0.339 (Fisher's exact test), Q value = 0.66
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 36 |
subtype1 | 2 | 7 |
subtype2 | 5 | 8 |
subtype3 | 5 | 14 |
subtype4 | 0 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 6 | 5 | 5 | 6 | 6 | 5 |
P value = 0.346 (logrank test), Q value = 0.66
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 32 | 6 | 0.0 - 211.2 (24.7) |
subtype1 | 5 | 1 | 4.3 - 31.7 (14.0) |
subtype2 | 5 | 2 | 1.9 - 45.1 (18.2) |
subtype3 | 5 | 1 | 4.1 - 26.0 (22.3) |
subtype4 | 6 | 0 | 23.6 - 196.6 (34.7) |
subtype5 | 6 | 1 | 25.1 - 211.2 (33.8) |
subtype6 | 5 | 1 | 0.0 - 70.1 (12.8) |
P value = 0.933 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 54.8 (14.2) |
subtype1 | 6 | 59.2 (13.7) |
subtype2 | 5 | 55.0 (15.7) |
subtype3 | 5 | 57.8 (12.3) |
subtype4 | 6 | 53.7 (16.8) |
subtype5 | 6 | 53.0 (16.2) |
subtype6 | 5 | 50.0 (14.7) |
P value = 0.457 (Fisher's exact test), Q value = 0.72
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 1 | 2 | 2 | 1 | 2 | 1 | 1 | 1 | 3 | 2 | 1 |
subtype1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 2 | 2 | 0 |
subtype2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
subtype4 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype5 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 |
subtype6 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
P value = 0.746 (Fisher's exact test), Q value = 0.95
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 18 |
subtype1 | 2 | 4 |
subtype2 | 2 | 3 |
subtype3 | 4 | 1 |
subtype4 | 3 | 3 |
subtype5 | 2 | 4 |
subtype6 | 2 | 3 |
P value = 0.322 (Fisher's exact test), Q value = 0.64
nPatients | NO | YES |
---|---|---|
ALL | 27 | 5 |
subtype1 | 6 | 0 |
subtype2 | 3 | 2 |
subtype3 | 5 | 0 |
subtype4 | 4 | 2 |
subtype5 | 5 | 1 |
subtype6 | 4 | 0 |
P value = 0.183 (Fisher's exact test), Q value = 0.52
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 27 | 2 | 4 |
subtype1 | 6 | 0 | 0 |
subtype2 | 4 | 0 | 1 |
subtype3 | 5 | 0 | 0 |
subtype4 | 5 | 0 | 1 |
subtype5 | 4 | 0 | 2 |
subtype6 | 3 | 2 | 0 |
P value = 0.19 (Fisher's exact test), Q value = 0.52
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 17 |
subtype1 | 3 | 3 |
subtype2 | 2 | 3 |
subtype3 | 5 | 0 |
subtype4 | 3 | 3 |
subtype5 | 2 | 4 |
subtype6 | 1 | 4 |
P value = 0.399 (Fisher's exact test), Q value = 0.71
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 26 |
subtype1 | 0 | 6 |
subtype2 | 2 | 3 |
subtype3 | 0 | 5 |
subtype4 | 2 | 4 |
subtype5 | 1 | 5 |
subtype6 | 2 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 15 | 12 |
P value = 0.306 (logrank test), Q value = 0.63
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 = 0.572 (Kruskal-Wallis (anova)), Q value = 0.84
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 33 | 54.8 (14.2) |
subtype1 | 6 | 55.2 (16.9) |
subtype2 | 15 | 52.3 (14.7) |
subtype3 | 12 | 57.8 (12.6) |
P value = 0.393 (Fisher's exact test), Q value = 0.71
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 1 | 2 | 2 | 1 | 2 | 1 | 1 | 1 | 3 | 2 | 1 |
subtype1 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
subtype2 | 1 | 0 | 1 | 0 | 1 | 2 | 0 | 1 | 0 | 2 | 1 | 0 |
subtype3 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
P value = 0.902 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 15 | 18 |
subtype1 | 3 | 3 |
subtype2 | 6 | 9 |
subtype3 | 6 | 6 |
P value = 0.83 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 27 | 5 |
subtype1 | 5 | 0 |
subtype2 | 12 | 3 |
subtype3 | 10 | 2 |
P value = 0.427 (Fisher's exact test), Q value = 0.71
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 27 | 2 | 4 |
subtype1 | 5 | 1 | 0 |
subtype2 | 12 | 0 | 3 |
subtype3 | 10 | 1 | 1 |
P value = 0.277 (Fisher's exact test), Q value = 0.6
nPatients | ASIAN | WHITE |
---|---|---|
ALL | 16 | 17 |
subtype1 | 1 | 5 |
subtype2 | 8 | 7 |
subtype3 | 7 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 7 | 26 |
subtype1 | 1 | 5 |
subtype2 | 3 | 12 |
subtype3 | 3 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 10 | 12 | 9 | 3 | 8 | 6 |
P value = 0.917 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 9 | 2 | 0.0 - 211.2 (27.4) |
subtype2 | 12 | 2 | 1.9 - 128.1 (33.6) |
subtype3 | 9 | 1 | 4.1 - 57.2 (14.0) |
subtype4 | 3 | 1 | 8.2 - 52.0 (32.3) |
subtype5 | 8 | 2 | 0.6 - 116.8 (33.8) |
subtype6 | 6 | 1 | 12.8 - 70.1 (38.6) |
P value = 0.437 (Kruskal-Wallis (anova)), Q value = 0.71
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 56.3 (13.9) |
subtype1 | 10 | 57.2 (10.4) |
subtype2 | 12 | 57.2 (13.3) |
subtype3 | 9 | 57.8 (12.0) |
subtype4 | 3 | 62.3 (6.1) |
subtype5 | 8 | 59.1 (18.3) |
subtype6 | 6 | 43.7 (17.2) |
P value = 0.0405 (Fisher's exact test), Q value = 0.33
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 2 |
subtype1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 2 | 2 |
subtype2 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
subtype3 | 2 | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
subtype4 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype5 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
subtype6 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
P value = 0.446 (Fisher's exact test), Q value = 0.71
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 22 |
subtype1 | 4 | 6 |
subtype2 | 6 | 6 |
subtype3 | 4 | 5 |
subtype4 | 3 | 0 |
subtype5 | 6 | 2 |
subtype6 | 3 | 3 |
P value = 0.226 (Fisher's exact test), Q value = 0.55
nPatients | NO | YES |
---|---|---|
ALL | 40 | 7 |
subtype1 | 8 | 1 |
subtype2 | 10 | 2 |
subtype3 | 8 | 1 |
subtype4 | 3 | 0 |
subtype5 | 8 | 0 |
subtype6 | 3 | 3 |
P value = 0.0365 (Fisher's exact test), Q value = 0.33
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 41 | 3 | 4 |
subtype1 | 9 | 1 | 0 |
subtype2 | 12 | 0 | 0 |
subtype3 | 8 | 1 | 0 |
subtype4 | 3 | 0 | 0 |
subtype5 | 6 | 1 | 1 |
subtype6 | 3 | 0 | 3 |
P value = 0.21 (Fisher's exact test), Q value = 0.54
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 29 |
subtype1 | 4 | 0 | 6 |
subtype2 | 5 | 1 | 6 |
subtype3 | 6 | 0 | 3 |
subtype4 | 1 | 0 | 2 |
subtype5 | 2 | 0 | 6 |
subtype6 | 0 | 0 | 6 |
P value = 0.083 (Fisher's exact test), Q value = 0.42
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 36 |
subtype1 | 0 | 10 |
subtype2 | 3 | 9 |
subtype3 | 2 | 7 |
subtype4 | 1 | 2 |
subtype5 | 2 | 6 |
subtype6 | 4 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 22 | 11 | 7 | 8 |
P value = 0.302 (logrank test), Q value = 0.63
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 21 | 3 | 0.6 - 211.2 (31.7) |
subtype2 | 11 | 2 | 1.9 - 128.1 (41.2) |
subtype3 | 7 | 2 | 0.0 - 52.0 (23.3) |
subtype4 | 8 | 2 | 9.8 - 57.2 (23.8) |
P value = 0.682 (Kruskal-Wallis (anova)), Q value = 0.9
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 48 | 56.3 (13.9) |
subtype1 | 22 | 57.5 (13.3) |
subtype2 | 11 | 57.8 (13.8) |
subtype3 | 7 | 57.9 (11.2) |
subtype4 | 8 | 49.5 (18.2) |
P value = 0.0603 (Fisher's exact test), Q value = 0.4
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 2 |
subtype1 | 0 | 1 | 0 | 2 | 0 | 2 | 0 | 1 | 0 | 2 | 0 | 2 | 2 |
subtype2 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
subtype3 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
subtype4 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
P value = 0.974 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 22 |
subtype1 | 11 | 11 |
subtype2 | 6 | 5 |
subtype3 | 4 | 3 |
subtype4 | 5 | 3 |
P value = 0.0886 (Fisher's exact test), Q value = 0.42
nPatients | NO | YES |
---|---|---|
ALL | 40 | 7 |
subtype1 | 21 | 1 |
subtype2 | 9 | 2 |
subtype3 | 5 | 1 |
subtype4 | 5 | 3 |
P value = 0.0795 (Fisher's exact test), Q value = 0.42
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 41 | 3 | 4 |
subtype1 | 19 | 2 | 1 |
subtype2 | 11 | 0 | 0 |
subtype3 | 6 | 1 | 0 |
subtype4 | 5 | 0 | 3 |
P value = 0.854 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 29 |
subtype1 | 8 | 0 | 14 |
subtype2 | 4 | 1 | 6 |
subtype3 | 3 | 0 | 4 |
subtype4 | 3 | 0 | 5 |
P value = 0.209 (Fisher's exact test), Q value = 0.54
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 36 |
subtype1 | 3 | 19 |
subtype2 | 3 | 8 |
subtype3 | 2 | 5 |
subtype4 | 4 | 4 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 16 | 16 | 15 |
P value = 0.684 (logrank test), Q value = 0.9
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 46 | 9 | 0.0 - 211.2 (26.7) |
subtype1 | 15 | 3 | 0.0 - 211.2 (27.4) |
subtype2 | 16 | 4 | 1.9 - 116.8 (33.8) |
subtype3 | 15 | 2 | 9.8 - 128.1 (24.6) |
P value = 0.855 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 56.3 (14.1) |
subtype1 | 16 | 56.4 (13.1) |
subtype2 | 16 | 57.6 (15.2) |
subtype3 | 15 | 54.7 (14.8) |
P value = 0.103 (Fisher's exact test), Q value = 0.42
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 1 |
subtype1 | 0 | 1 | 2 | 2 | 0 | 0 | 0 | 1 | 0 | 3 | 1 | 2 | 0 |
subtype2 | 0 | 1 | 1 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 2 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
P value = 0.581 (Fisher's exact test), Q value = 0.84
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 22 |
subtype1 | 7 | 9 |
subtype2 | 10 | 6 |
subtype3 | 8 | 7 |
P value = 0.0671 (Fisher's exact test), Q value = 0.41
nPatients | NO | YES |
---|---|---|
ALL | 40 | 6 |
subtype1 | 13 | 2 |
subtype2 | 16 | 0 |
subtype3 | 11 | 4 |
P value = 0.233 (Fisher's exact test), Q value = 0.55
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 | 12 | 3 | 1 |
subtype2 | 15 | 0 | 1 |
subtype3 | 13 | 0 | 2 |
P value = 0.73 (Fisher's exact test), Q value = 0.94
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 28 |
subtype1 | 5 | 0 | 11 |
subtype2 | 7 | 1 | 8 |
subtype3 | 6 | 0 | 9 |
P value = 0.0365 (Fisher's exact test), Q value = 0.33
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 35 |
subtype1 | 4 | 12 |
subtype2 | 1 | 15 |
subtype3 | 7 | 8 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 9 | 12 | 8 | 12 | 6 |
P value = 0.511 (logrank test), Q value = 0.78
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 = 0.888 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 47 | 56.3 (14.1) |
subtype1 | 9 | 56.3 (10.4) |
subtype2 | 12 | 58.8 (12.6) |
subtype3 | 8 | 57.4 (9.1) |
subtype4 | 12 | 56.2 (18.9) |
subtype5 | 6 | 49.8 (18.3) |
P value = 0.901 (Fisher's exact test), Q value = 1
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | SOFT TISSUE (MUSCLE LIGAMENTS SUBCUTANEOUS) | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 1 | 2 | 1 |
subtype1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
subtype2 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 | 0 |
subtype4 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 |
subtype5 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
P value = 0.171 (Fisher's exact test), Q value = 0.52
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 22 |
subtype1 | 2 | 7 |
subtype2 | 8 | 4 |
subtype3 | 4 | 4 |
subtype4 | 6 | 6 |
subtype5 | 5 | 1 |
P value = 0.138 (Fisher's exact test), Q value = 0.48
nPatients | NO | YES |
---|---|---|
ALL | 40 | 6 |
subtype1 | 9 | 0 |
subtype2 | 10 | 2 |
subtype3 | 7 | 0 |
subtype4 | 8 | 4 |
subtype5 | 6 | 0 |
P value = 0.0401 (Fisher's exact test), Q value = 0.33
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 | 9 | 0 | 0 |
subtype2 | 10 | 0 | 2 |
subtype3 | 5 | 3 | 0 |
subtype4 | 11 | 0 | 1 |
subtype5 | 5 | 0 | 1 |
P value = 0.982 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 18 | 1 | 28 |
subtype1 | 4 | 0 | 5 |
subtype2 | 4 | 1 | 7 |
subtype3 | 3 | 0 | 5 |
subtype4 | 4 | 0 | 8 |
subtype5 | 3 | 0 | 3 |
P value = 0.0177 (Fisher's exact test), Q value = 0.33
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 35 |
subtype1 | 0 | 9 |
subtype2 | 3 | 9 |
subtype3 | 2 | 6 |
subtype4 | 7 | 5 |
subtype5 | 0 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 10 | 9 | 14 |
P value = 0.986 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 41 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 8 | 1 | 0.0 - 196.6 (18.7) |
subtype2 | 10 | 2 | 1.9 - 111.6 (33.4) |
subtype3 | 9 | 2 | 8.2 - 128.1 (26.0) |
subtype4 | 14 | 4 | 4.1 - 211.2 (33.8) |
P value = 0.798 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 55.1 (14.0) |
subtype1 | 9 | 58.2 (10.7) |
subtype2 | 10 | 53.8 (19.3) |
subtype3 | 9 | 57.2 (12.5) |
subtype4 | 14 | 52.6 (13.2) |
P value = 0.411 (Fisher's exact test), Q value = 0.71
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 2 | 1 |
subtype1 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 |
subtype2 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
subtype4 | 0 | 1 | 1 | 0 | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 1 |
P value = 0.186 (Fisher's exact test), Q value = 0.52
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 20 |
subtype1 | 3 | 6 |
subtype2 | 6 | 4 |
subtype3 | 3 | 6 |
subtype4 | 10 | 4 |
P value = 0.0398 (Fisher's exact test), Q value = 0.33
nPatients | NO | YES |
---|---|---|
ALL | 36 | 5 |
subtype1 | 8 | 0 |
subtype2 | 8 | 2 |
subtype3 | 6 | 3 |
subtype4 | 14 | 0 |
P value = 0.0197 (Fisher's exact test), Q value = 0.33
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 36 | 3 | 3 |
subtype1 | 6 | 3 | 0 |
subtype2 | 8 | 0 | 2 |
subtype3 | 9 | 0 | 0 |
subtype4 | 13 | 0 | 1 |
P value = 0.145 (Fisher's exact test), Q value = 0.48
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 16 | 1 | 25 |
subtype1 | 3 | 0 | 6 |
subtype2 | 1 | 0 | 9 |
subtype3 | 5 | 0 | 4 |
subtype4 | 7 | 1 | 6 |
P value = 0.0189 (Fisher's exact test), Q value = 0.33
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 32 |
subtype1 | 2 | 7 |
subtype2 | 4 | 6 |
subtype3 | 4 | 5 |
subtype4 | 0 | 14 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 8 | 15 | 5 | 14 |
P value = 0.969 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 41 | 9 | 0.0 - 211.2 (27.4) |
subtype1 | 7 | 1 | 0.6 - 196.6 (22.3) |
subtype2 | 15 | 4 | 1.9 - 128.1 (42.7) |
subtype3 | 5 | 1 | 10.3 - 38.2 (26.0) |
subtype4 | 14 | 3 | 0.0 - 211.2 (29.2) |
P value = 0.223 (Kruskal-Wallis (anova)), Q value = 0.55
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 55.1 (14.0) |
subtype1 | 8 | 58.9 (11.0) |
subtype2 | 15 | 50.5 (17.9) |
subtype3 | 5 | 65.2 (7.5) |
subtype4 | 14 | 54.2 (10.6) |
P value = 0.0472 (Fisher's exact test), Q value = 0.34
nPatients | ADRENAL | ASCITES/PERITONEUM | BONE | BRAIN | BREAST | COLON | LIVER | OTHER EXTRANODAL SITE | PAROTID GLAND | SMALL INTESTINE | STOMACH | THYROID |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 2 | 4 | 3 | 1 | 2 | 1 | 1 | 1 | 3 | 2 | 1 |
subtype1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 1 |
subtype2 | 0 | 2 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
subtype3 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
subtype4 | 1 | 0 | 2 | 0 | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 0 |
P value = 0.659 (Fisher's exact test), Q value = 0.89
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 20 |
subtype1 | 3 | 5 |
subtype2 | 8 | 7 |
subtype3 | 2 | 3 |
subtype4 | 9 | 5 |
P value = 0.0934 (Fisher's exact test), Q value = 0.42
nPatients | NO | YES |
---|---|---|
ALL | 36 | 5 |
subtype1 | 8 | 0 |
subtype2 | 11 | 4 |
subtype3 | 4 | 1 |
subtype4 | 13 | 0 |
P value = 0.125 (Fisher's exact test), Q value = 0.46
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 36 | 3 | 3 |
subtype1 | 6 | 2 | 0 |
subtype2 | 12 | 0 | 3 |
subtype3 | 5 | 0 | 0 |
subtype4 | 13 | 1 | 0 |
P value = 0.106 (Fisher's exact test), Q value = 0.42
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 16 | 1 | 25 |
subtype1 | 3 | 0 | 5 |
subtype2 | 2 | 1 | 12 |
subtype3 | 3 | 0 | 2 |
subtype4 | 8 | 0 | 6 |
P value = 0.0272 (Fisher's exact test), Q value = 0.33
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 10 | 32 |
subtype1 | 2 | 6 |
subtype2 | 6 | 9 |
subtype3 | 2 | 3 |
subtype4 | 0 | 14 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/22541055/DLBC-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/22506396/DLBC-TP.merged_data.txt
-
Number of patients = 48
-
Number of clustering approaches = 10
-
Number of selected clinical features = 8
-
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.