This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 6 different clustering approaches and 4 clinical features across 73 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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3 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 sequencing-based mRNA expression data identified 7 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 2 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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2 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
COMPLETENESS OF RESECTION |
Statistical Tests | logrank test | t-test | Fisher's exact test | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.434 (1.00) |
0.943 (1.00) |
0.24 (1.00) |
0.505 (1.00) |
METHLYATION CNMF |
0.729 (1.00) |
0.0508 (1.00) |
0.521 (1.00) |
0.557 (1.00) |
RNAseq CNMF subtypes |
0.862 (1.00) |
0.141 (1.00) |
0.0734 (1.00) |
0.374 (1.00) |
RNAseq cHierClus subtypes |
0.838 (1.00) |
0.0219 (0.526) |
0.0366 (0.843) |
0.411 (1.00) |
MIRSEQ CNMF |
0.287 (1.00) |
0.0533 (1.00) |
0.207 (1.00) |
0.534 (1.00) |
MIRSEQ CHIERARCHICAL |
0.974 (1.00) |
0.75 (1.00) |
0.246 (1.00) |
0.221 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 26 | 28 |
P value = 0.434 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 66 | 26 | 0.1 - 90.7 (13.2) |
subtype1 | 17 | 7 | 0.1 - 90.7 (7.3) |
subtype2 | 23 | 8 | 0.1 - 79.4 (19.8) |
subtype3 | 26 | 11 | 0.1 - 83.6 (11.3) |
P value = 0.943 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 60.7 (14.4) |
subtype1 | 17 | 59.7 (15.3) |
subtype2 | 26 | 61.3 (14.1) |
subtype3 | 27 | 60.7 (14.6) |
P value = 0.24 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 47 |
subtype1 | 4 | 14 |
subtype2 | 12 | 14 |
subtype3 | 9 | 19 |
P value = 0.505 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 50 | 8 | 1 | 8 |
subtype1 | 12 | 3 | 1 | 1 |
subtype2 | 18 | 2 | 0 | 2 |
subtype3 | 20 | 3 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 20 | 21 | 31 |
P value = 0.729 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 65 | 25 | 0.1 - 90.7 (12.8) |
subtype1 | 16 | 8 | 0.4 - 90.7 (22.5) |
subtype2 | 19 | 7 | 0.1 - 66.3 (6.3) |
subtype3 | 30 | 10 | 0.1 - 83.6 (8.3) |
P value = 0.0508 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 59.9 (14.9) |
subtype1 | 19 | 58.5 (17.0) |
subtype2 | 21 | 54.4 (16.2) |
subtype3 | 30 | 64.5 (11.1) |
P value = 0.521 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 26 | 46 |
subtype1 | 9 | 11 |
subtype2 | 8 | 13 |
subtype3 | 9 | 22 |
P value = 0.557 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 49 | 8 | 1 | 9 |
subtype1 | 13 | 3 | 0 | 1 |
subtype2 | 15 | 1 | 1 | 4 |
subtype3 | 21 | 4 | 0 | 4 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|
Number of samples | 16 | 7 | 6 | 11 | 11 | 3 | 4 | 1 | 1 |
P value = 0.862 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 23 | 0.1 - 83.6 (14.3) |
subtype1 | 13 | 7 | 3.0 - 49.0 (19.8) |
subtype2 | 7 | 3 | 0.1 - 55.2 (10.1) |
subtype3 | 5 | 2 | 6.0 - 46.8 (14.3) |
subtype4 | 11 | 7 | 0.3 - 83.6 (23.3) |
subtype5 | 11 | 4 | 0.6 - 79.4 (6.7) |
subtype6 | 3 | 0 | 1.2 - 13.8 (8.3) |
subtype7 | 4 | 0 | 0.1 - 34.1 (15.6) |
P value = 0.141 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 58 | 60.1 (14.5) |
subtype1 | 16 | 57.0 (16.7) |
subtype2 | 7 | 54.7 (13.7) |
subtype3 | 6 | 61.8 (12.5) |
subtype4 | 11 | 67.9 (8.5) |
subtype5 | 11 | 61.5 (14.0) |
subtype6 | 3 | 69.0 (5.6) |
subtype7 | 4 | 47.0 (19.6) |
P value = 0.0734 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 22 | 36 |
subtype1 | 8 | 8 |
subtype2 | 4 | 3 |
subtype3 | 1 | 5 |
subtype4 | 5 | 6 |
subtype5 | 0 | 11 |
subtype6 | 2 | 1 |
subtype7 | 2 | 2 |
P value = 0.374 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 41 | 7 | 1 | 6 |
subtype1 | 8 | 4 | 0 | 3 |
subtype2 | 6 | 0 | 1 | 0 |
subtype3 | 5 | 0 | 0 | 0 |
subtype4 | 8 | 1 | 0 | 2 |
subtype5 | 9 | 1 | 0 | 0 |
subtype6 | 2 | 1 | 0 | 0 |
subtype7 | 3 | 0 | 0 | 1 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 26 | 34 |
P value = 0.838 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 23 | 0.1 - 83.6 (14.3) |
subtype1 | 23 | 8 | 0.1 - 55.2 (14.9) |
subtype2 | 32 | 15 | 0.3 - 83.6 (14.0) |
P value = 0.0219 (t-test), Q value = 0.53
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 59 | 59.7 (14.7) |
subtype1 | 26 | 54.5 (16.7) |
subtype2 | 33 | 63.7 (11.6) |
P value = 0.0366 (Fisher's exact test), Q value = 0.84
nPatients | FEMALE | MALE |
---|---|---|
ALL | 23 | 37 |
subtype1 | 14 | 12 |
subtype2 | 9 | 25 |
P value = 0.411 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 43 | 7 | 1 | 6 |
subtype1 | 17 | 4 | 0 | 4 |
subtype2 | 26 | 3 | 1 | 2 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 28 | 14 | 29 |
P value = 0.287 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 64 | 25 | 0.1 - 83.6 (13.2) |
subtype1 | 25 | 11 | 0.1 - 69.6 (14.3) |
subtype2 | 11 | 6 | 1.1 - 83.6 (8.3) |
subtype3 | 28 | 8 | 0.3 - 79.4 (16.8) |
P value = 0.0533 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 60.3 (14.9) |
subtype1 | 28 | 55.4 (15.2) |
subtype2 | 12 | 60.8 (17.6) |
subtype3 | 29 | 64.9 (12.1) |
P value = 0.207 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 46 |
subtype1 | 11 | 17 |
subtype2 | 2 | 12 |
subtype3 | 12 | 17 |
P value = 0.534 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 48 | 8 | 1 | 9 |
subtype1 | 20 | 3 | 1 | 4 |
subtype2 | 6 | 3 | 0 | 2 |
subtype3 | 22 | 2 | 0 | 3 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 8 | 63 |
P value = 0.974 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 64 | 25 | 0.1 - 83.6 (13.2) |
subtype1 | 6 | 3 | 1.1 - 83.6 (7.4) |
subtype2 | 58 | 22 | 0.1 - 79.4 (14.0) |
P value = 0.75 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 69 | 60.3 (14.9) |
subtype1 | 8 | 58.5 (16.9) |
subtype2 | 61 | 60.6 (14.7) |
P value = 0.246 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 25 | 46 |
subtype1 | 1 | 7 |
subtype2 | 24 | 39 |
P value = 0.221 (Chi-square test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 48 | 8 | 1 | 9 |
subtype1 | 3 | 2 | 0 | 0 |
subtype2 | 45 | 6 | 1 | 9 |
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Cluster data file = LIHC-TP.mergedcluster.txt
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Clinical data file = LIHC-TP.clin.merged.picked.txt
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Number of patients = 73
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Number of clustering approaches = 6
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Number of selected clinical features = 4
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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 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 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.