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 8 clinical features across 95 patients, 11 significant findings detected with P value < 0.05.
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CNMF clustering analysis on array-based mRNA expression data identified 2 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on array-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'Time to Death', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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CNMF clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'TUMOR.STAGE'.
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Consensus hierarchical clustering analysis on sequencing-based miR expression data identified 3 subtypes that correlate to 'PATHOLOGY.T'.
Clinical Features |
Statistical Tests |
mRNA CNMF subtypes |
mRNA cHierClus subtypes |
METHLYATION CNMF |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRseq CNMF subtypes |
MIRseq cHierClus subtypes |
Time to Death | logrank test | 0.666 | 0.0699 | 0.0501 | 0.0626 | 0.0122 | 0.282 | 0.373 |
AGE | ANOVA | 0.182 | 0.948 | 0.00254 | 0.434 | 0.246 | 0.716 | 0.908 |
GENDER | Fisher's exact test | 0.585 | 1 | 0.306 | 0.0644 | 0.0625 | 0.175 | 0.0887 |
KARNOFSKY PERFORMANCE SCORE | ANOVA | 0.241 | 0.481 | 0.282 | 0.665 | |||
PATHOLOGY T | Chi-square test | 0.0623 | 0.216 | 9.15e-08 | 0.00023 | 0.37 | 0.12 | 0.0193 |
PATHOLOGY N | Chi-square test | 0.145 | 0.934 | 0.0693 | 0.247 | 0.242 | ||
PATHOLOGICSPREAD(M) | Chi-square test | 1 | 1 | 0.0476 | 0.108 | 0.0402 | 0.3 | 0.309 |
TUMOR STAGE | Chi-square test | 0.292 | 3.75e-06 | 0.000784 | 0.00334 | 0.026 | 0.0681 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 7 | 9 |
P value = 0.666 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 2 | 0.5 - 58.5 (7.8) |
subtype1 | 7 | 1 | 0.5 - 53.8 (5.9) |
subtype2 | 9 | 1 | 1.1 - 58.5 (10.8) |
P value = 0.182 (t-test)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 57.9 (11.5) |
subtype1 | 7 | 53.6 (10.3) |
subtype2 | 9 | 61.3 (11.7) |
P value = 0.585 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 12 |
subtype1 | 1 | 6 |
subtype2 | 3 | 6 |
P value = 0.0623 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 7 | 2 |
subtype1 | 1 | 4 | 2 |
subtype2 | 6 | 3 | 0 |
P value = 1 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 9 | 1 |
subtype1 | 4 | 1 |
subtype2 | 5 | 0 |
P value = 0.292 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 5 | 2 | 1 | 1 |
subtype1 | 1 | 1 | 1 | 1 |
subtype2 | 4 | 1 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 4 | 7 | 5 |
P value = 0.0699 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 16 | 2 | 0.5 - 58.5 (7.8) |
subtype1 | 4 | 1 | 10.8 - 58.5 (40.4) |
subtype2 | 7 | 1 | 0.5 - 25.1 (4.4) |
subtype3 | 5 | 0 | 0.7 - 53.8 (4.1) |
P value = 0.948 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 16 | 57.9 (11.5) |
subtype1 | 4 | 57.0 (5.0) |
subtype2 | 7 | 57.4 (13.0) |
subtype3 | 5 | 59.4 (14.8) |
P value = 1 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 12 |
subtype1 | 1 | 3 |
subtype2 | 2 | 5 |
subtype3 | 1 | 4 |
P value = 0.216 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 7 | 7 | 2 |
subtype1 | 3 | 1 | 0 |
subtype2 | 1 | 4 | 2 |
subtype3 | 3 | 2 | 0 |
P value = 1 (Fisher's exact test)
nPatients | M0 | M1 |
---|---|---|
ALL | 9 | 1 |
subtype1 | 2 | 0 |
subtype2 | 4 | 1 |
subtype3 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 37 | 19 | 23 |
P value = 0.0501 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 72 | 12 | 0.0 - 182.7 (20.9) |
subtype1 | 33 | 2 | 0.0 - 129.9 (15.5) |
subtype2 | 17 | 4 | 0.7 - 80.8 (26.3) |
subtype3 | 22 | 6 | 0.9 - 182.7 (19.7) |
P value = 0.00254 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 76 | 60.5 (12.0) |
subtype1 | 36 | 56.4 (9.8) |
subtype2 | 18 | 67.9 (8.7) |
subtype3 | 22 | 61.2 (14.6) |
P value = 0.306 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 24 | 55 |
subtype1 | 8 | 29 |
subtype2 | 7 | 12 |
subtype3 | 9 | 14 |
P value = 0.241 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 19 | 92.1 (13.6) |
subtype1 | 14 | 95.7 (5.1) |
subtype2 | 4 | 77.5 (25.0) |
subtype3 | 1 | 100.0 (NA) |
P value = 9.15e-08 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 47 | 3 | 29 |
subtype1 | 30 | 3 | 4 |
subtype2 | 14 | 0 | 5 |
subtype3 | 3 | 0 | 20 |
P value = 0.145 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 19 | 8 | 4 |
subtype1 | 8 | 0 | 0 |
subtype2 | 3 | 2 | 1 |
subtype3 | 8 | 6 | 3 |
P value = 0.0476 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 45 | 4 | 27 |
subtype1 | 17 | 0 | 17 |
subtype2 | 12 | 1 | 6 |
subtype3 | 16 | 3 | 4 |
P value = 3.75e-06 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 44 | 3 | 21 | 8 |
subtype1 | 28 | 2 | 4 | 0 |
subtype2 | 13 | 1 | 3 | 2 |
subtype3 | 3 | 0 | 14 | 6 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 22 | 18 | 12 | 11 |
P value = 0.0626 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 63 | 13 | 0.5 - 123.6 (15.5) |
subtype1 | 22 | 7 | 0.9 - 93.3 (16.2) |
subtype2 | 18 | 2 | 0.5 - 63.7 (12.6) |
subtype3 | 12 | 2 | 7.0 - 123.6 (29.1) |
subtype4 | 11 | 2 | 3.8 - 80.8 (15.5) |
P value = 0.434 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 63 | 60.3 (12.5) |
subtype1 | 22 | 59.2 (14.2) |
subtype2 | 18 | 58.7 (11.7) |
subtype3 | 12 | 65.8 (11.2) |
subtype4 | 11 | 59.3 (11.6) |
P value = 0.0644 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 43 |
subtype1 | 11 | 11 |
subtype2 | 6 | 12 |
subtype3 | 1 | 11 |
subtype4 | 2 | 9 |
P value = 0.00023 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 32 | 8 | 23 |
subtype1 | 6 | 1 | 15 |
subtype2 | 10 | 5 | 3 |
subtype3 | 5 | 2 | 5 |
subtype4 | 11 | 0 | 0 |
P value = 0.934 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 14 | 9 | 3 |
subtype1 | 7 | 6 | 2 |
subtype2 | 2 | 1 | 0 |
subtype3 | 4 | 2 | 1 |
subtype4 | 1 | 0 | 0 |
P value = 0.108 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 42 | 5 | 9 |
subtype1 | 14 | 5 | 3 |
subtype2 | 10 | 0 | 2 |
subtype3 | 11 | 0 | 1 |
subtype4 | 7 | 0 | 3 |
P value = 0.000784 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 29 | 3 | 16 | 7 |
subtype1 | 5 | 1 | 8 | 7 |
subtype2 | 9 | 0 | 3 | 0 |
subtype3 | 5 | 2 | 5 | 0 |
subtype4 | 10 | 0 | 0 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 16 | 25 | 22 |
P value = 0.0122 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 63 | 13 | 0.5 - 123.6 (15.5) |
subtype1 | 16 | 6 | 2.8 - 80.8 (10.9) |
subtype2 | 25 | 3 | 0.5 - 123.6 (13.6) |
subtype3 | 22 | 4 | 6.4 - 93.3 (25.2) |
P value = 0.246 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 63 | 60.3 (12.5) |
subtype1 | 16 | 59.1 (13.4) |
subtype2 | 25 | 58.0 (11.3) |
subtype3 | 22 | 63.9 (13.1) |
P value = 0.0625 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 43 |
subtype1 | 9 | 7 |
subtype2 | 6 | 19 |
subtype3 | 5 | 17 |
P value = 0.481 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 83.8 (34.2) |
subtype1 | 3 | 93.3 (5.8) |
subtype2 | 5 | 78.0 (43.8) |
P value = 0.37 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 32 | 8 | 23 |
subtype1 | 7 | 2 | 7 |
subtype2 | 14 | 5 | 6 |
subtype3 | 11 | 1 | 10 |
P value = 0.0693 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 14 | 9 | 3 |
subtype1 | 1 | 5 | 2 |
subtype2 | 4 | 2 | 0 |
subtype3 | 9 | 2 | 1 |
P value = 0.0402 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 42 | 5 | 9 |
subtype1 | 8 | 4 | 3 |
subtype2 | 15 | 1 | 4 |
subtype3 | 19 | 0 | 2 |
P value = 0.00334 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 29 | 3 | 16 | 7 |
subtype1 | 6 | 1 | 1 | 6 |
subtype2 | 13 | 1 | 5 | 1 |
subtype3 | 10 | 1 | 10 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 33 | 33 | 29 |
P value = 0.282 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 88 | 14 | 0.0 - 182.7 (15.7) |
subtype1 | 32 | 4 | 0.0 - 96.9 (25.6) |
subtype2 | 31 | 7 | 0.7 - 182.7 (20.1) |
subtype3 | 25 | 3 | 0.1 - 123.6 (12.7) |
P value = 0.716 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 60.1 (11.9) |
subtype1 | 33 | 60.3 (12.7) |
subtype2 | 33 | 58.8 (12.7) |
subtype3 | 26 | 61.3 (9.8) |
P value = 0.175 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 67 |
subtype1 | 6 | 27 |
subtype2 | 13 | 20 |
subtype3 | 9 | 20 |
P value = 0.282 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 87.5 (24.5) |
subtype1 | 7 | 94.3 (5.3) |
subtype2 | 9 | 77.8 (34.6) |
subtype3 | 4 | 97.5 (5.0) |
P value = 0.12 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 54 | 10 | 31 |
subtype1 | 18 | 2 | 13 |
subtype2 | 18 | 2 | 13 |
subtype3 | 18 | 6 | 5 |
P value = 0.247 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 19 | 10 | 4 |
subtype1 | 9 | 3 | 1 |
subtype2 | 5 | 6 | 3 |
subtype3 | 5 | 1 | 0 |
P value = 0.3 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 27 |
subtype1 | 22 | 0 | 9 |
subtype2 | 19 | 4 | 10 |
subtype3 | 13 | 1 | 8 |
P value = 0.026 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 49 | 5 | 22 | 9 |
subtype1 | 17 | 2 | 12 | 0 |
subtype2 | 17 | 2 | 5 | 8 |
subtype3 | 15 | 1 | 5 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 19 | 37 | 39 |
P value = 0.373 (logrank test)
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 88 | 14 | 0.0 - 182.7 (15.7) |
subtype1 | 17 | 2 | 0.1 - 123.6 (12.7) |
subtype2 | 33 | 7 | 0.6 - 182.7 (22.9) |
subtype3 | 38 | 5 | 0.0 - 96.9 (20.4) |
P value = 0.908 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 60.1 (11.9) |
subtype1 | 17 | 61.0 (10.3) |
subtype2 | 36 | 60.2 (12.1) |
subtype3 | 39 | 59.5 (12.6) |
P value = 0.0887 (Fisher's exact test)
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 67 |
subtype1 | 6 | 13 |
subtype2 | 15 | 22 |
subtype3 | 7 | 32 |
P value = 0.665 (ANOVA)
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 20 | 87.5 (24.5) |
subtype1 | 3 | 96.7 (5.8) |
subtype2 | 10 | 89.0 (17.9) |
subtype3 | 7 | 81.4 (36.3) |
P value = 0.0193 (Chi-square test)
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 54 | 10 | 31 |
subtype1 | 13 | 5 | 1 |
subtype2 | 20 | 2 | 15 |
subtype3 | 21 | 3 | 15 |
P value = 0.242 (Chi-square test)
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 19 | 10 | 4 |
subtype1 | 2 | 0 | 0 |
subtype2 | 6 | 6 | 3 |
subtype3 | 11 | 4 | 1 |
P value = 0.309 (Chi-square test)
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 27 |
subtype1 | 10 | 0 | 5 |
subtype2 | 19 | 4 | 13 |
subtype3 | 25 | 1 | 9 |
P value = 0.0681 (Chi-square test)
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 49 | 5 | 22 | 9 |
subtype1 | 10 | 1 | 2 | 0 |
subtype2 | 19 | 2 | 7 | 8 |
subtype3 | 20 | 2 | 13 | 1 |
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Cluster data file = KIRP.mergedcluster.txt
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Clinical data file = KIRP.clin.merged.picked.txt
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Number of patients = 95
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Number of clustering approaches = 7
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Number of selected clinical features = 8
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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, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.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
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 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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.