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 7 clinical features across 13 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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2 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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2 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
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2 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.
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2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.0414 (1.00) |
0.237 (1.00) |
0.11 (1.00) |
0.00673 (0.283) |
0.331 (1.00) |
0.331 (1.00) |
AGE | t-test |
0.391 (1.00) |
0.628 (1.00) |
0.178 (1.00) |
0.109 (1.00) |
0.643 (1.00) |
0.643 (1.00) |
NEOPLASM DISEASESTAGE | Fisher's exact test |
0.529 (1.00) |
0.237 (1.00) |
0.464 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
PATHOLOGY T STAGE | Fisher's exact test |
0.266 (1.00) |
0.266 (1.00) |
0.0476 (1.00) |
0.143 (1.00) |
0.206 (1.00) |
0.206 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
1 (1.00) |
1 (1.00) |
0.5 (1.00) |
0.429 (1.00) |
0.444 (1.00) |
0.444 (1.00) |
PATHOLOGY M STAGE | Fisher's exact test |
0.559 (1.00) |
0.559 (1.00) |
0.5 (1.00) |
0.429 (1.00) |
1 (1.00) |
1 (1.00) |
GENDER | Fisher's exact test |
1 (1.00) |
1 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.167 (1.00) |
0.167 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 6 | 7 |
P value = 0.0414 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 13 | 10 | 1.9 - 91.7 (18.8) |
subtype1 | 6 | 5 | 1.9 - 23.3 (15.5) |
subtype2 | 7 | 5 | 5.2 - 91.7 (43.3) |
P value = 0.391 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 13 | 61.1 (8.0) |
subtype1 | 6 | 59.0 (5.3) |
subtype2 | 7 | 62.9 (9.8) |
P value = 0.529 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III |
---|---|---|---|
ALL | 1 | 5 | 7 |
subtype1 | 0 | 2 | 4 |
subtype2 | 1 | 3 | 3 |
P value = 0.266 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 9 | 4 |
subtype1 | 3 | 3 |
subtype2 | 6 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 10 | 3 |
subtype1 | 5 | 1 |
subtype2 | 5 | 2 |
P value = 0.559 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 9 | 4 |
subtype1 | 5 | 1 |
subtype2 | 4 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 9 |
subtype1 | 2 | 4 |
subtype2 | 2 | 5 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 7 | 6 |
P value = 0.237 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 13 | 10 | 1.9 - 91.7 (18.8) |
subtype1 | 7 | 5 | 13.6 - 91.7 (23.3) |
subtype2 | 6 | 5 | 1.9 - 80.8 (8.1) |
P value = 0.628 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 13 | 61.1 (8.0) |
subtype1 | 7 | 60.0 (7.4) |
subtype2 | 6 | 62.3 (9.1) |
P value = 0.237 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III |
---|---|---|---|
ALL | 1 | 5 | 7 |
subtype1 | 0 | 4 | 3 |
subtype2 | 1 | 1 | 4 |
P value = 0.266 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 9 | 4 |
subtype1 | 6 | 1 |
subtype2 | 3 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 10 | 3 |
subtype1 | 5 | 2 |
subtype2 | 5 | 1 |
P value = 0.559 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 9 | 4 |
subtype1 | 4 | 3 |
subtype2 | 5 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 4 | 9 |
subtype1 | 2 | 5 |
subtype2 | 2 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 6 | 3 |
P value = 0.11 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 9 | 7 | 1.9 - 51.8 (13.6) |
subtype1 | 6 | 4 | 1.9 - 51.8 (16.2) |
subtype2 | 3 | 3 | 3.5 - 17.3 (5.2) |
P value = 0.178 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 9 | 61.6 (8.1) |
subtype1 | 6 | 59.5 (9.4) |
subtype2 | 3 | 65.7 (2.3) |
P value = 0.464 (Fisher's exact test), Q value = 1
nPatients | STAGE II | STAGE III |
---|---|---|
ALL | 3 | 6 |
subtype1 | 3 | 3 |
subtype2 | 0 | 3 |
P value = 0.0476 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 5 | 4 |
subtype1 | 5 | 1 |
subtype2 | 0 | 3 |
P value = 0.5 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 7 | 2 |
subtype1 | 4 | 2 |
subtype2 | 3 | 0 |
P value = 0.5 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 7 | 2 |
subtype1 | 4 | 2 |
subtype2 | 3 | 0 |
P value = 0.464 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 3 | 6 |
subtype1 | 3 | 3 |
subtype2 | 0 | 3 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 4 | 4 | 1 |
P value = 0.00673 (logrank test), Q value = 0.28
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 8 | 6 | 1.9 - 51.8 (12.3) |
subtype1 | 4 | 4 | 1.9 - 10.9 (4.4) |
subtype2 | 4 | 2 | 13.6 - 51.8 (21.1) |
P value = 0.109 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 8 | 60.9 (8.4) |
subtype1 | 4 | 66.0 (9.2) |
subtype2 | 4 | 55.8 (3.0) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | STAGE II | STAGE III |
---|---|---|
ALL | 3 | 5 |
subtype1 | 1 | 3 |
subtype2 | 2 | 2 |
P value = 0.143 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 5 | 3 |
subtype1 | 1 | 3 |
subtype2 | 4 | 0 |
P value = 0.429 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 6 | 2 |
subtype1 | 4 | 0 |
subtype2 | 2 | 2 |
P value = 0.429 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 6 | 2 |
subtype1 | 4 | 0 |
subtype2 | 2 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 3 | 5 |
subtype1 | 1 | 3 |
subtype2 | 2 | 2 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 5 | 4 |
P value = 0.331 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 9 | 7 | 1.9 - 51.8 (13.6) |
subtype1 | 5 | 4 | 1.9 - 51.8 (18.8) |
subtype2 | 4 | 3 | 3.5 - 17.3 (9.4) |
P value = 0.643 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 9 | 61.6 (8.1) |
subtype1 | 5 | 60.4 (10.2) |
subtype2 | 4 | 63.0 (5.7) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | STAGE II | STAGE III |
---|---|---|
ALL | 3 | 6 |
subtype1 | 2 | 3 |
subtype2 | 1 | 3 |
P value = 0.206 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 5 | 4 |
subtype1 | 4 | 1 |
subtype2 | 1 | 3 |
P value = 0.444 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 7 | 2 |
subtype1 | 3 | 2 |
subtype2 | 4 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 7 | 2 |
subtype1 | 4 | 1 |
subtype2 | 3 | 1 |
P value = 0.167 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 3 | 6 |
subtype1 | 3 | 2 |
subtype2 | 0 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 4 | 5 |
P value = 0.331 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 9 | 7 | 1.9 - 51.8 (13.6) |
subtype1 | 4 | 3 | 3.5 - 17.3 (9.4) |
subtype2 | 5 | 4 | 1.9 - 51.8 (18.8) |
P value = 0.643 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 9 | 61.6 (8.1) |
subtype1 | 4 | 63.0 (5.7) |
subtype2 | 5 | 60.4 (10.2) |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | STAGE II | STAGE III |
---|---|---|
ALL | 3 | 6 |
subtype1 | 1 | 3 |
subtype2 | 2 | 3 |
P value = 0.206 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3 |
---|---|---|
ALL | 5 | 4 |
subtype1 | 1 | 3 |
subtype2 | 4 | 1 |
P value = 0.444 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 7 | 2 |
subtype1 | 4 | 0 |
subtype2 | 3 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 7 | 2 |
subtype1 | 3 | 1 |
subtype2 | 4 | 1 |
P value = 0.167 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 3 | 6 |
subtype1 | 0 | 4 |
subtype2 | 3 | 2 |
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Cluster data file = MESO-TP.mergedcluster.txt
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Clinical data file = MESO-TP.merged_data.txt
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Number of patients = 13
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Number of clustering approaches = 6
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Number of selected clinical features = 7
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Exclude small clusters that include fewer than K patients, K = 3
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 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
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.