This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 7 different clustering approaches and 5 clinical features across 852 patients, 12 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 8 subtypes that correlate to 'Time to Death' and 'AGE'.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that correlate to 'AGE'.
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6 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death' and 'AGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'AGE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death' and 'AGE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'Time to Death' and 'AGE'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 5 subtypes that correlate to 'Time to Death' and 'AGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
Statistical Tests | logrank test | ANOVA | Chi-square test | Chi-square test | Chi-square test |
mRNA CNMF subtypes | 0.00106 | 2.3e-06 | 0.0519 | 0.897 | 0.391 |
mRNA cHierClus subtypes | 0.557 | 0.00176 | 0.322 | 0.195 | 0.335 |
METHLYATION CNMF | 0.00169 | 3.91e-07 | 0.0642 | 0.291 | 0.932 |
RNAseq CNMF subtypes | 0.179 | 0.00573 | 0.0991 | 0.467 | 0.184 |
RNAseq cHierClus subtypes | 0.00841 | 0.000672 | 0.0886 | 0.255 | 0.0533 |
MIRseq CNMF subtypes | 0.0145 | 0.00623 | 0.152 | 0.964 | 0.263 |
MIRseq cHierClus subtypes | 0.0244 | 0.0124 | 0.382 | 0.225 | 0.146 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 126 | 41 | 21 | 103 | 107 | 73 | 20 | 38 |
P value = 0.00106 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 497 | 65 | 0.1 - 223.4 (24.1) |
subtype1 | 116 | 17 | 0.1 - 177.4 (24.4) |
subtype2 | 40 | 4 | 0.1 - 157.4 (40.6) |
subtype3 | 19 | 3 | 0.3 - 223.4 (14.0) |
subtype4 | 98 | 12 | 0.1 - 211.5 (21.9) |
subtype5 | 104 | 10 | 0.3 - 220.9 (19.0) |
subtype6 | 64 | 14 | 0.1 - 189.0 (24.9) |
subtype7 | 19 | 2 | 0.2 - 97.5 (36.3) |
subtype8 | 37 | 3 | 0.3 - 82.7 (20.0) |
P value = 2.3e-06 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 529 | 57.9 (13.2) |
subtype1 | 126 | 58.5 (14.3) |
subtype2 | 41 | 50.0 (12.1) |
subtype3 | 21 | 59.4 (13.8) |
subtype4 | 103 | 53.8 (12.6) |
subtype5 | 107 | 62.1 (12.4) |
subtype6 | 73 | 58.5 (12.5) |
subtype7 | 20 | 60.4 (9.9) |
subtype8 | 38 | 60.3 (12.0) |
P value = 0.0519 (Chi-square test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 523 | 6 |
subtype1 | 122 | 4 |
subtype2 | 41 | 0 |
subtype3 | 20 | 1 |
subtype4 | 103 | 0 |
subtype5 | 107 | 0 |
subtype6 | 73 | 0 |
subtype7 | 19 | 1 |
subtype8 | 38 | 0 |
P value = 0.897 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 147 | 382 |
subtype1 | 33 | 93 |
subtype2 | 11 | 30 |
subtype3 | 4 | 17 |
subtype4 | 34 | 69 |
subtype5 | 29 | 78 |
subtype6 | 19 | 54 |
subtype7 | 5 | 15 |
subtype8 | 12 | 26 |
P value = 0.391 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 221 | 308 |
subtype1 | 53 | 73 |
subtype2 | 20 | 21 |
subtype3 | 5 | 16 |
subtype4 | 48 | 55 |
subtype5 | 45 | 62 |
subtype6 | 26 | 47 |
subtype7 | 6 | 14 |
subtype8 | 18 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 129 | 129 | 271 |
P value = 0.557 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 497 | 65 | 0.1 - 223.4 (24.1) |
subtype1 | 118 | 15 | 0.1 - 211.5 (21.6) |
subtype2 | 125 | 14 | 0.3 - 157.4 (27.2) |
subtype3 | 254 | 36 | 0.1 - 223.4 (23.1) |
P value = 0.00176 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 529 | 57.9 (13.2) |
subtype1 | 129 | 55.1 (12.6) |
subtype2 | 129 | 56.7 (13.1) |
subtype3 | 271 | 59.8 (13.4) |
P value = 0.322 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 523 | 6 |
subtype1 | 129 | 0 |
subtype2 | 128 | 1 |
subtype3 | 266 | 5 |
P value = 0.195 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 147 | 382 |
subtype1 | 43 | 86 |
subtype2 | 37 | 92 |
subtype3 | 67 | 204 |
P value = 0.335 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 221 | 308 |
subtype1 | 59 | 70 |
subtype2 | 57 | 72 |
subtype3 | 105 | 166 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 89 | 139 | 94 | 95 | 33 | 89 |
P value = 0.00169 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 510 | 61 | 0.0 - 223.4 (17.9) |
subtype1 | 83 | 13 | 0.2 - 211.5 (17.2) |
subtype2 | 130 | 10 | 0.3 - 223.4 (13.2) |
subtype3 | 92 | 16 | 0.0 - 109.9 (14.2) |
subtype4 | 90 | 10 | 0.1 - 177.4 (23.4) |
subtype5 | 32 | 4 | 4.3 - 157.4 (20.9) |
subtype6 | 83 | 8 | 0.0 - 194.3 (25.7) |
P value = 3.91e-07 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 538 | 57.6 (13.1) |
subtype1 | 89 | 55.5 (12.9) |
subtype2 | 139 | 59.0 (12.3) |
subtype3 | 94 | 63.8 (12.0) |
subtype4 | 95 | 53.6 (14.7) |
subtype5 | 33 | 54.7 (13.1) |
subtype6 | 88 | 56.0 (11.4) |
P value = 0.0642 (Chi-square test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 533 | 6 |
subtype1 | 89 | 0 |
subtype2 | 138 | 1 |
subtype3 | 92 | 2 |
subtype4 | 94 | 1 |
subtype5 | 31 | 2 |
subtype6 | 89 | 0 |
P value = 0.291 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 134 | 405 |
subtype1 | 29 | 60 |
subtype2 | 33 | 106 |
subtype3 | 20 | 74 |
subtype4 | 27 | 68 |
subtype5 | 5 | 28 |
subtype6 | 20 | 69 |
P value = 0.932 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 202 | 337 |
subtype1 | 35 | 54 |
subtype2 | 55 | 84 |
subtype3 | 34 | 60 |
subtype4 | 37 | 58 |
subtype5 | 11 | 22 |
subtype6 | 30 | 59 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 234 | 147 | 422 |
P value = 0.179 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 748 | 92 | 0.0 - 223.4 (19.0) |
subtype1 | 215 | 32 | 0.0 - 211.5 (19.2) |
subtype2 | 142 | 13 | 0.3 - 194.3 (28.6) |
subtype3 | 391 | 47 | 0.0 - 223.4 (17.0) |
P value = 0.00573 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 802 | 58.0 (13.1) |
subtype1 | 234 | 57.0 (12.8) |
subtype2 | 146 | 55.7 (12.3) |
subtype3 | 422 | 59.3 (13.5) |
P value = 0.0991 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 795 | 8 |
subtype1 | 234 | 0 |
subtype2 | 146 | 1 |
subtype3 | 415 | 7 |
P value = 0.467 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 191 | 612 |
subtype1 | 57 | 177 |
subtype2 | 40 | 107 |
subtype3 | 94 | 328 |
P value = 0.184 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 298 | 505 |
subtype1 | 86 | 148 |
subtype2 | 64 | 83 |
subtype3 | 148 | 274 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 235 | 376 | 192 |
P value = 0.00841 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 748 | 92 | 0.0 - 223.4 (19.0) |
subtype1 | 229 | 19 | 0.1 - 194.3 (25.4) |
subtype2 | 343 | 47 | 0.0 - 223.4 (17.0) |
subtype3 | 176 | 26 | 0.0 - 211.5 (19.1) |
P value = 0.000672 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 802 | 58.0 (13.1) |
subtype1 | 234 | 56.2 (12.2) |
subtype2 | 376 | 59.9 (13.6) |
subtype3 | 192 | 56.4 (12.8) |
P value = 0.0886 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 795 | 8 |
subtype1 | 234 | 1 |
subtype2 | 369 | 7 |
subtype3 | 192 | 0 |
P value = 0.255 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 191 | 612 |
subtype1 | 59 | 176 |
subtype2 | 80 | 296 |
subtype3 | 52 | 140 |
P value = 0.0533 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 298 | 505 |
subtype1 | 101 | 134 |
subtype2 | 125 | 251 |
subtype3 | 72 | 120 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 199 | 393 | 215 |
P value = 0.0145 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 748 | 92 | 0.0 - 223.4 (19.0) |
subtype1 | 190 | 20 | 0.3 - 159.1 (23.0) |
subtype2 | 364 | 40 | 0.0 - 223.4 (18.0) |
subtype3 | 194 | 32 | 0.0 - 211.5 (18.0) |
P value = 0.00623 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 806 | 58.2 (13.2) |
subtype1 | 198 | 56.2 (12.5) |
subtype2 | 393 | 59.6 (13.6) |
subtype3 | 215 | 57.4 (12.9) |
P value = 0.152 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 798 | 9 |
subtype1 | 199 | 0 |
subtype2 | 386 | 7 |
subtype3 | 213 | 2 |
P value = 0.964 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 188 | 619 |
subtype1 | 45 | 154 |
subtype2 | 92 | 301 |
subtype3 | 51 | 164 |
P value = 0.263 (Fisher's exact test)
nPatients | NO | YES |
---|---|---|
ALL | 298 | 509 |
subtype1 | 82 | 117 |
subtype2 | 144 | 249 |
subtype3 | 72 | 143 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 178 | 181 | 187 | 229 | 32 |
P value = 0.0244 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 748 | 92 | 0.0 - 223.4 (19.0) |
subtype1 | 169 | 27 | 0.1 - 211.5 (19.5) |
subtype2 | 159 | 19 | 0.1 - 223.4 (16.5) |
subtype3 | 170 | 24 | 0.0 - 189.0 (17.8) |
subtype4 | 222 | 19 | 0.1 - 177.4 (20.3) |
subtype5 | 28 | 3 | 0.5 - 113.8 (34.2) |
P value = 0.0124 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 806 | 58.2 (13.2) |
subtype1 | 178 | 56.3 (12.9) |
subtype2 | 181 | 59.7 (15.0) |
subtype3 | 187 | 59.4 (12.4) |
subtype4 | 228 | 58.3 (12.2) |
subtype5 | 32 | 52.9 (14.5) |
P value = 0.382 (Chi-square test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 798 | 9 |
subtype1 | 177 | 1 |
subtype2 | 177 | 4 |
subtype3 | 184 | 3 |
subtype4 | 228 | 1 |
subtype5 | 32 | 0 |
P value = 0.225 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 188 | 619 |
subtype1 | 42 | 136 |
subtype2 | 47 | 134 |
subtype3 | 34 | 153 |
subtype4 | 54 | 175 |
subtype5 | 11 | 21 |
P value = 0.146 (Chi-square test)
nPatients | NO | YES |
---|---|---|
ALL | 298 | 509 |
subtype1 | 64 | 114 |
subtype2 | 67 | 114 |
subtype3 | 57 | 130 |
subtype4 | 95 | 134 |
subtype5 | 15 | 17 |
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Cluster data file = BRCA.mergedcluster.txt
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Clinical data file = BRCA.clin.merged.picked.txt
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Number of patients = 852
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Number of clustering approaches = 7
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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 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 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 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.