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 6 clinical features across 211 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.
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CNMF clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-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 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'AGE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
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4 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death', 'AGE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 5 subtypes that correlate to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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6 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Chi-square test | Fisher's exact test |
mRNA CNMF subtypes |
0.247 (1.00) |
0.326 (1.00) |
0.101 (1.00) |
0.441 (1.00) |
0.0226 (0.902) |
0.893 (1.00) |
mRNA cHierClus subtypes |
0.0482 (1.00) |
0.35 (1.00) |
0.122 (1.00) |
0.205 (1.00) |
0.0109 (0.448) |
0.788 (1.00) |
Copy Number Ratio CNMF subtypes |
1.62e-05 (0.000841) |
6.39e-08 (3.58e-06) |
0.00183 (0.0823) |
0.977 (1.00) |
2.47e-13 (1.45e-11) |
0.28 (1.00) |
METHLYATION CNMF |
6.62e-06 (0.000357) |
4.31e-07 (2.37e-05) |
0.075 (1.00) |
0.617 (1.00) |
2.76e-14 (1.65e-12) |
0.000952 (0.0457) |
RNAseq CNMF subtypes |
1.74e-05 (0.000886) |
0.00125 (0.0589) |
0.0091 (0.391) |
0.327 (1.00) |
8.84e-11 (5.13e-09) |
0.705 (1.00) |
RNAseq cHierClus subtypes |
0.0328 (1.00) |
0.0419 (1.00) |
0.444 (1.00) |
0.245 (1.00) |
2.28e-10 (1.3e-08) |
0.19 (1.00) |
MIRSEQ CNMF |
0.105 (1.00) |
0.524 (1.00) |
0.256 (1.00) |
0.597 (1.00) |
1.06e-05 (0.00056) |
0.342 (1.00) |
MIRSEQ CHIERARCHICAL |
0.0382 (1.00) |
0.68 (1.00) |
0.579 (1.00) |
0.497 (1.00) |
0.00175 (0.0806) |
0.934 (1.00) |
MIRseq Mature CNMF subtypes |
0.00745 (0.328) |
0.0104 (0.439) |
0.288 (1.00) |
0.351 (1.00) |
0.000187 (0.00937) |
0.643 (1.00) |
MIRseq Mature cHierClus subtypes |
0.024 (0.935) |
0.449 (1.00) |
0.29 (1.00) |
0.659 (1.00) |
0.000268 (0.0131) |
0.524 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 9 | 10 | 8 |
P value = 0.247 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 9 | 0.1 - 134.3 (46.6) |
subtype1 | 9 | 4 | 10.6 - 130.8 (43.9) |
subtype2 | 10 | 3 | 0.1 - 78.2 (36.5) |
subtype3 | 8 | 2 | 14.4 - 134.3 (51.3) |
P value = 0.326 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 39.3 (9.1) |
subtype1 | 9 | 39.2 (6.2) |
subtype2 | 10 | 42.3 (7.6) |
subtype3 | 8 | 35.8 (12.6) |
P value = 0.101 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 18 |
subtype1 | 2 | 7 |
subtype2 | 6 | 4 |
subtype3 | 1 | 7 |
P value = 0.441 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 88.8 (12.2) |
subtype1 | 7 | 84.3 (16.2) |
subtype2 | 7 | 92.9 (7.6) |
subtype3 | 3 | 90.0 (10.0) |
P value = 0.0226 (Chi-square test), Q value = 0.9
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 10 | 9 | 8 |
subtype1 | 7 | 2 | 0 |
subtype2 | 2 | 3 | 5 |
subtype3 | 1 | 4 | 3 |
P value = 0.893 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 15 | 12 |
subtype1 | 5 | 4 |
subtype2 | 5 | 5 |
subtype3 | 5 | 3 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 7 | 6 | 10 | 4 |
P value = 0.0482 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 27 | 9 | 0.1 - 134.3 (46.6) |
subtype1 | 7 | 1 | 0.1 - 78.2 (31.8) |
subtype2 | 6 | 1 | 14.4 - 134.3 (52.7) |
subtype3 | 10 | 5 | 10.6 - 130.8 (37.1) |
subtype4 | 4 | 2 | 20.0 - 47.9 (43.9) |
P value = 0.35 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 39.3 (9.1) |
subtype1 | 7 | 43.9 (8.6) |
subtype2 | 6 | 34.8 (14.6) |
subtype3 | 10 | 39.6 (6.0) |
subtype4 | 4 | 37.5 (3.4) |
P value = 0.122 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 9 | 18 |
subtype1 | 5 | 2 |
subtype2 | 1 | 5 |
subtype3 | 2 | 8 |
subtype4 | 1 | 3 |
P value = 0.205 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 88.8 (12.2) |
subtype1 | 5 | 94.0 (8.9) |
subtype2 | 2 | 90.0 (14.1) |
subtype3 | 8 | 85.0 (15.1) |
subtype4 | 2 | 90.0 (0.0) |
P value = 0.0109 (Chi-square test), Q value = 0.45
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 10 | 9 | 8 |
subtype1 | 1 | 1 | 5 |
subtype2 | 0 | 4 | 2 |
subtype3 | 7 | 2 | 1 |
subtype4 | 2 | 2 | 0 |
P value = 0.788 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 15 | 12 |
subtype1 | 3 | 4 |
subtype2 | 3 | 3 |
subtype3 | 6 | 4 |
subtype4 | 3 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 85 | 48 | 74 |
P value = 1.62e-05 (logrank test), Q value = 0.00084
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
subtype1 | 85 | 14 | 0.1 - 156.2 (13.4) |
subtype2 | 48 | 24 | 0.5 - 211.2 (11.9) |
subtype3 | 73 | 13 | 0.0 - 182.3 (14.3) |
P value = 6.39e-08 (ANOVA), Q value = 3.6e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
subtype1 | 85 | 37.3 (11.8) |
subtype2 | 48 | 50.1 (12.9) |
subtype3 | 74 | 45.2 (12.9) |
P value = 0.00183 (Fisher's exact test), Q value = 0.082
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 118 |
subtype1 | 28 | 57 |
subtype2 | 31 | 17 |
subtype3 | 30 | 44 |
P value = 0.977 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 93 | 88.4 (10.5) |
subtype1 | 37 | 88.6 (10.8) |
subtype2 | 26 | 88.1 (7.5) |
subtype3 | 30 | 88.3 (12.3) |
P value = 2.47e-13 (Chi-square test), Q value = 1.5e-11
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
subtype1 | 33 | 30 | 21 |
subtype2 | 24 | 15 | 9 |
subtype3 | 6 | 9 | 59 |
P value = 0.28 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 127 |
subtype1 | 38 | 47 |
subtype2 | 18 | 30 |
subtype3 | 24 | 50 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 92 | 31 | 27 | 56 |
P value = 6.62e-06 (logrank test), Q value = 0.00036
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 205 | 47 | 0.0 - 211.2 (13.3) |
subtype1 | 92 | 21 | 0.0 - 156.2 (16.9) |
subtype2 | 31 | 16 | 0.1 - 211.2 (8.4) |
subtype3 | 27 | 2 | 0.1 - 97.9 (10.6) |
subtype4 | 55 | 8 | 0.1 - 182.3 (12.4) |
P value = 4.31e-07 (ANOVA), Q value = 2.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 206 | 42.9 (13.3) |
subtype1 | 92 | 38.8 (11.7) |
subtype2 | 31 | 52.6 (12.8) |
subtype3 | 27 | 39.4 (13.2) |
subtype4 | 56 | 46.1 (12.9) |
P value = 0.075 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 90 | 116 |
subtype1 | 33 | 59 |
subtype2 | 19 | 12 |
subtype3 | 14 | 13 |
subtype4 | 24 | 32 |
P value = 0.617 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 88.5 (10.5) |
subtype1 | 47 | 89.6 (10.4) |
subtype2 | 15 | 87.3 (5.9) |
subtype3 | 7 | 84.3 (7.9) |
subtype4 | 23 | 88.3 (13.4) |
P value = 2.76e-14 (Chi-square test), Q value = 1.7e-12
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 55 | 87 |
subtype1 | 35 | 35 | 21 |
subtype2 | 20 | 5 | 6 |
subtype3 | 7 | 8 | 12 |
subtype4 | 1 | 7 | 48 |
P value = 0.000952 (Fisher's exact test), Q value = 0.046
nPatients | NO | YES |
---|---|---|
ALL | 77 | 129 |
subtype1 | 48 | 44 |
subtype2 | 10 | 21 |
subtype3 | 6 | 21 |
subtype4 | 13 | 43 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 55 | 40 | 35 | 67 | 9 |
P value = 1.74e-05 (logrank test), Q value = 0.00089
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 205 | 51 | 0.0 - 211.2 (13.4) |
subtype1 | 55 | 14 | 0.0 - 130.8 (16.5) |
subtype2 | 40 | 20 | 0.1 - 211.2 (9.6) |
subtype3 | 34 | 8 | 0.1 - 182.3 (15.8) |
subtype4 | 67 | 8 | 0.1 - 156.2 (14.5) |
subtype5 | 9 | 1 | 0.2 - 44.0 (14.3) |
P value = 0.00125 (ANOVA), Q value = 0.059
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 206 | 43.2 (13.4) |
subtype1 | 55 | 38.8 (11.7) |
subtype2 | 40 | 48.1 (14.0) |
subtype3 | 35 | 47.5 (12.5) |
subtype4 | 67 | 42.5 (13.8) |
subtype5 | 9 | 36.2 (10.5) |
P value = 0.0091 (Chi-square test), Q value = 0.39
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 117 |
subtype1 | 19 | 36 |
subtype2 | 26 | 14 |
subtype3 | 18 | 17 |
subtype4 | 24 | 43 |
subtype5 | 2 | 7 |
P value = 0.327 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 91 | 88.2 (10.5) |
subtype1 | 32 | 90.9 (9.3) |
subtype2 | 18 | 87.8 (5.5) |
subtype3 | 16 | 86.9 (15.4) |
subtype4 | 22 | 86.8 (9.9) |
subtype5 | 3 | 80.0 (17.3) |
P value = 8.84e-11 (Chi-square test), Q value = 5.1e-09
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 62 | 54 | 89 |
subtype1 | 20 | 20 | 15 |
subtype2 | 28 | 6 | 6 |
subtype3 | 2 | 5 | 28 |
subtype4 | 10 | 20 | 36 |
subtype5 | 2 | 3 | 4 |
P value = 0.705 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 78 | 128 |
subtype1 | 24 | 31 |
subtype2 | 15 | 25 |
subtype3 | 10 | 25 |
subtype4 | 26 | 41 |
subtype5 | 3 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 32 | 108 | 66 |
P value = 0.0328 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 205 | 51 | 0.0 - 211.2 (13.4) |
subtype1 | 31 | 8 | 0.1 - 182.3 (15.1) |
subtype2 | 108 | 33 | 0.0 - 211.2 (12.9) |
subtype3 | 66 | 10 | 0.1 - 156.2 (14.5) |
P value = 0.0419 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 206 | 43.2 (13.4) |
subtype1 | 32 | 48.6 (12.4) |
subtype2 | 108 | 42.0 (13.2) |
subtype3 | 66 | 42.5 (13.7) |
P value = 0.444 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 117 |
subtype1 | 17 | 15 |
subtype2 | 46 | 62 |
subtype3 | 26 | 40 |
P value = 0.245 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 91 | 88.2 (10.5) |
subtype1 | 16 | 86.9 (15.4) |
subtype2 | 52 | 89.8 (9.0) |
subtype3 | 23 | 85.7 (9.5) |
P value = 2.28e-10 (Chi-square test), Q value = 1.3e-08
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 62 | 54 | 89 |
subtype1 | 1 | 4 | 27 |
subtype2 | 51 | 31 | 25 |
subtype3 | 10 | 19 | 37 |
P value = 0.19 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 78 | 128 |
subtype1 | 8 | 24 |
subtype2 | 46 | 62 |
subtype3 | 24 | 42 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 55 | 32 | 77 | 43 |
P value = 0.105 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 50 | 0.0 - 211.2 (13.4) |
subtype1 | 55 | 14 | 0.0 - 117.4 (8.4) |
subtype2 | 32 | 6 | 0.1 - 182.3 (21.2) |
subtype3 | 76 | 13 | 0.1 - 138.2 (12.9) |
subtype4 | 43 | 17 | 0.1 - 211.2 (16.8) |
P value = 0.524 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.2 (13.4) |
subtype1 | 55 | 43.1 (14.3) |
subtype2 | 32 | 43.2 (10.6) |
subtype3 | 77 | 44.6 (13.9) |
subtype4 | 43 | 40.8 (13.2) |
P value = 0.256 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 118 |
subtype1 | 22 | 33 |
subtype2 | 19 | 13 |
subtype3 | 31 | 46 |
subtype4 | 17 | 26 |
P value = 0.597 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 88.5 (10.5) |
subtype1 | 24 | 90.8 (8.8) |
subtype2 | 19 | 88.4 (13.4) |
subtype3 | 29 | 86.9 (9.7) |
subtype4 | 20 | 88.0 (10.6) |
P value = 1.06e-05 (Chi-square test), Q value = 0.00056
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
subtype1 | 26 | 13 | 15 |
subtype2 | 3 | 7 | 22 |
subtype3 | 13 | 23 | 41 |
subtype4 | 21 | 11 | 11 |
P value = 0.342 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 127 |
subtype1 | 21 | 34 |
subtype2 | 9 | 23 |
subtype3 | 29 | 48 |
subtype4 | 21 | 22 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 8 | 89 | 110 |
P value = 0.0382 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 50 | 0.0 - 211.2 (13.4) |
subtype1 | 8 | 1 | 7.1 - 52.4 (13.8) |
subtype2 | 88 | 13 | 0.1 - 211.2 (12.4) |
subtype3 | 110 | 36 | 0.0 - 182.3 (15.6) |
P value = 0.68 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.2 (13.4) |
subtype1 | 8 | 42.1 (14.0) |
subtype2 | 89 | 44.2 (13.8) |
subtype3 | 110 | 42.5 (13.1) |
P value = 0.579 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 118 |
subtype1 | 3 | 5 |
subtype2 | 42 | 47 |
subtype3 | 44 | 66 |
P value = 0.497 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 88.5 (10.5) |
subtype1 | 4 | 87.5 (5.0) |
subtype2 | 36 | 86.9 (11.9) |
subtype3 | 52 | 89.6 (9.7) |
P value = 0.00175 (Chi-square test), Q value = 0.081
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
subtype1 | 4 | 2 | 2 |
subtype2 | 15 | 23 | 51 |
subtype3 | 44 | 29 | 36 |
P value = 0.934 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 127 |
subtype1 | 3 | 5 |
subtype2 | 33 | 56 |
subtype3 | 44 | 66 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 36 | 27 | 66 | 31 | 28 | 19 |
P value = 0.00745 (logrank test), Q value = 0.33
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 50 | 0.0 - 211.2 (13.4) |
subtype1 | 36 | 15 | 0.2 - 117.4 (12.4) |
subtype2 | 27 | 3 | 0.1 - 130.8 (17.5) |
subtype3 | 65 | 11 | 0.1 - 156.2 (13.4) |
subtype4 | 31 | 12 | 0.1 - 211.2 (17.9) |
subtype5 | 28 | 7 | 0.1 - 133.7 (6.2) |
subtype6 | 19 | 2 | 0.0 - 95.6 (6.5) |
P value = 0.0104 (ANOVA), Q value = 0.44
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.2 (13.4) |
subtype1 | 36 | 46.7 (14.5) |
subtype2 | 27 | 43.9 (10.4) |
subtype3 | 66 | 43.2 (13.9) |
subtype4 | 31 | 47.3 (13.8) |
subtype5 | 28 | 38.9 (12.6) |
subtype6 | 19 | 35.5 (9.3) |
P value = 0.288 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 118 |
subtype1 | 15 | 21 |
subtype2 | 14 | 13 |
subtype3 | 29 | 37 |
subtype4 | 17 | 14 |
subtype5 | 9 | 19 |
subtype6 | 5 | 14 |
P value = 0.351 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 88.5 (10.5) |
subtype1 | 19 | 92.6 (5.6) |
subtype2 | 15 | 88.7 (12.5) |
subtype3 | 26 | 85.4 (10.3) |
subtype4 | 16 | 87.5 (12.9) |
subtype5 | 10 | 90.0 (6.7) |
subtype6 | 6 | 88.3 (14.7) |
P value = 0.000187 (Chi-square test), Q value = 0.0094
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
subtype1 | 20 | 9 | 6 |
subtype2 | 7 | 5 | 15 |
subtype3 | 11 | 18 | 37 |
subtype4 | 6 | 9 | 16 |
subtype5 | 15 | 8 | 5 |
subtype6 | 4 | 5 | 10 |
P value = 0.643 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 127 |
subtype1 | 13 | 23 |
subtype2 | 12 | 15 |
subtype3 | 23 | 43 |
subtype4 | 14 | 17 |
subtype5 | 13 | 15 |
subtype6 | 5 | 14 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 6 | 109 | 92 |
P value = 0.024 (logrank test), Q value = 0.94
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 50 | 0.0 - 211.2 (13.4) |
subtype1 | 6 | 1 | 7.2 - 21.0 (13.8) |
subtype2 | 109 | 36 | 0.0 - 182.3 (15.4) |
subtype3 | 91 | 13 | 0.1 - 211.2 (12.4) |
P value = 0.449 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.2 (13.4) |
subtype1 | 6 | 43.2 (13.4) |
subtype2 | 109 | 42.1 (13.0) |
subtype3 | 92 | 44.5 (13.8) |
P value = 0.29 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 118 |
subtype1 | 2 | 4 |
subtype2 | 42 | 67 |
subtype3 | 45 | 47 |
P value = 0.659 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 88.5 (10.5) |
subtype1 | 4 | 87.5 (5.0) |
subtype2 | 50 | 89.4 (9.8) |
subtype3 | 38 | 87.4 (11.8) |
P value = 0.000268 (Chi-square test), Q value = 0.013
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
subtype1 | 3 | 0 | 3 |
subtype2 | 45 | 30 | 33 |
subtype3 | 15 | 24 | 53 |
P value = 0.524 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 80 | 127 |
subtype1 | 3 | 3 |
subtype2 | 45 | 64 |
subtype3 | 32 | 60 |
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Cluster data file = LGG-TP.mergedcluster.txt
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Clinical data file = LGG-TP.clin.merged.picked.txt
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Number of patients = 211
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Number of clustering approaches = 10
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Number of selected clinical features = 6
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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 continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.