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 5 clinical features across 200 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.
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4 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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5 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'Time to Death' and 'YEARS_TO_BIRTH'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'RACE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that correlate to 'Time to Death' and 'YEARS_TO_BIRTH'.
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5 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'Time to Death' and 'YEARS_TO_BIRTH'.
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3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
GENDER | RACE | ETHNICITY |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.667 (0.87) |
0.54 (0.787) |
0.317 (0.733) |
0.955 (1.00) |
0.556 (0.787) |
METHLYATION CNMF |
4.31e-07 (6.47e-06) |
4.2e-07 (6.47e-06) |
0.859 (0.991) |
0.287 (0.718) |
0.454 (0.761) |
RNAseq CNMF subtypes |
0.495 (0.781) |
0.442 (0.761) |
0.143 (0.436) |
0.0435 (0.187) |
0.577 (0.787) |
RNAseq cHierClus subtypes |
0.000473 (0.00296) |
3.26e-05 (0.000326) |
0.413 (0.761) |
0.145 (0.436) |
0.082 (0.308) |
MIRSEQ CNMF |
0.0151 (0.0753) |
0.000493 (0.00296) |
0.793 (0.952) |
0.763 (0.952) |
1 (1.00) |
MIRSEQ CHIERARCHICAL |
0.161 (0.438) |
0.457 (0.761) |
0.386 (0.761) |
0.957 (1.00) |
1 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 49 | 44 | 55 | 43 |
P value = 0.667 (logrank test), Q value = 0.87
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 178 | 116 | 0.0 - 94.1 (11.0) |
subtype1 | 48 | 34 | 0.0 - 84.1 (18.0) |
subtype2 | 42 | 29 | 0.0 - 82.1 (10.1) |
subtype3 | 48 | 29 | 0.0 - 94.1 (8.0) |
subtype4 | 40 | 24 | 0.0 - 75.1 (12.0) |
P value = 0.54 (Kruskal-Wallis (anova)), Q value = 0.79
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 191 | 55.2 (16.1) |
subtype1 | 49 | 53.4 (15.9) |
subtype2 | 44 | 55.7 (17.4) |
subtype3 | 55 | 54.1 (17.1) |
subtype4 | 43 | 58.2 (13.4) |
P value = 0.317 (Fisher's exact test), Q value = 0.73
nPatients | FEMALE | MALE |
---|---|---|
ALL | 87 | 104 |
subtype1 | 27 | 22 |
subtype2 | 18 | 26 |
subtype3 | 21 | 34 |
subtype4 | 21 | 22 |
P value = 0.955 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 14 | 173 |
subtype1 | 1 | 4 | 44 |
subtype2 | 0 | 4 | 38 |
subtype3 | 1 | 4 | 50 |
subtype4 | 0 | 2 | 41 |
P value = 0.556 (Fisher's exact test), Q value = 0.79
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 3 | 185 |
subtype1 | 2 | 47 |
subtype2 | 0 | 42 |
subtype3 | 1 | 54 |
subtype4 | 0 | 42 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 25 | 25 | 62 | 38 | 44 |
P value = 4.31e-07 (logrank test), Q value = 6.5e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 179 | 116 | 0.0 - 94.1 (12.0) |
subtype1 | 25 | 20 | 0.0 - 69.0 (7.0) |
subtype2 | 24 | 8 | 0.0 - 84.1 (22.0) |
subtype3 | 56 | 45 | 0.0 - 56.1 (10.5) |
subtype4 | 34 | 13 | 1.0 - 94.1 (20.5) |
subtype5 | 40 | 30 | 0.0 - 55.0 (9.0) |
P value = 4.2e-07 (Kruskal-Wallis (anova)), Q value = 6.5e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 194 | 55.1 (16.0) |
subtype1 | 25 | 55.3 (14.6) |
subtype2 | 25 | 49.0 (15.3) |
subtype3 | 62 | 63.1 (12.9) |
subtype4 | 38 | 44.4 (17.2) |
subtype5 | 44 | 56.5 (14.0) |
P value = 0.859 (Fisher's exact test), Q value = 0.99
nPatients | FEMALE | MALE |
---|---|---|
ALL | 89 | 105 |
subtype1 | 12 | 13 |
subtype2 | 13 | 12 |
subtype3 | 26 | 36 |
subtype4 | 16 | 22 |
subtype5 | 22 | 22 |
P value = 0.287 (Fisher's exact test), Q value = 0.72
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 13 | 177 |
subtype1 | 0 | 0 | 25 |
subtype2 | 0 | 3 | 21 |
subtype3 | 0 | 4 | 58 |
subtype4 | 1 | 1 | 35 |
subtype5 | 1 | 5 | 38 |
P value = 0.454 (Fisher's exact test), Q value = 0.76
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 190 |
subtype1 | 0 | 25 |
subtype2 | 0 | 24 |
subtype3 | 0 | 61 |
subtype4 | 1 | 36 |
subtype5 | 0 | 44 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 75 | 52 | 46 |
P value = 0.495 (logrank test), Q value = 0.78
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 160 | 103 | 0.0 - 94.1 (11.5) |
subtype1 | 69 | 43 | 0.0 - 94.1 (14.0) |
subtype2 | 50 | 33 | 0.0 - 75.1 (9.5) |
subtype3 | 41 | 27 | 0.0 - 62.0 (10.0) |
P value = 0.442 (Kruskal-Wallis (anova)), Q value = 0.76
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 173 | 55.3 (16.1) |
subtype1 | 75 | 54.6 (17.3) |
subtype2 | 52 | 57.8 (13.7) |
subtype3 | 46 | 53.5 (16.7) |
P value = 0.143 (Fisher's exact test), Q value = 0.44
nPatients | FEMALE | MALE |
---|---|---|
ALL | 80 | 93 |
subtype1 | 32 | 43 |
subtype2 | 21 | 31 |
subtype3 | 27 | 19 |
P value = 0.0435 (Fisher's exact test), Q value = 0.19
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 13 | 156 |
subtype1 | 1 | 3 | 69 |
subtype2 | 1 | 2 | 49 |
subtype3 | 0 | 8 | 38 |
P value = 0.577 (Fisher's exact test), Q value = 0.79
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 169 |
subtype1 | 0 | 72 |
subtype2 | 1 | 51 |
subtype3 | 0 | 46 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 16 | 14 | 15 | 58 | 26 | 44 |
P value = 0.000473 (logrank test), Q value = 0.003
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 160 | 103 | 0.0 - 94.1 (11.5) |
subtype1 | 16 | 5 | 0.0 - 62.0 (36.0) |
subtype2 | 14 | 5 | 0.9 - 75.1 (20.0) |
subtype3 | 12 | 5 | 6.0 - 94.1 (20.5) |
subtype4 | 53 | 41 | 0.0 - 73.0 (10.1) |
subtype5 | 25 | 15 | 0.0 - 62.0 (8.1) |
subtype6 | 40 | 32 | 0.0 - 69.0 (8.5) |
P value = 3.26e-05 (Kruskal-Wallis (anova)), Q value = 0.00033
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 173 | 55.3 (16.1) |
subtype1 | 16 | 47.8 (14.9) |
subtype2 | 14 | 57.7 (14.6) |
subtype3 | 15 | 36.6 (13.9) |
subtype4 | 58 | 59.8 (15.5) |
subtype5 | 26 | 53.3 (16.7) |
subtype6 | 44 | 58.7 (13.0) |
P value = 0.413 (Fisher's exact test), Q value = 0.76
nPatients | FEMALE | MALE |
---|---|---|
ALL | 80 | 93 |
subtype1 | 9 | 7 |
subtype2 | 6 | 8 |
subtype3 | 6 | 9 |
subtype4 | 22 | 36 |
subtype5 | 16 | 10 |
subtype6 | 21 | 23 |
P value = 0.145 (Fisher's exact test), Q value = 0.44
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 13 | 156 |
subtype1 | 0 | 2 | 13 |
subtype2 | 0 | 0 | 14 |
subtype3 | 0 | 0 | 15 |
subtype4 | 1 | 3 | 53 |
subtype5 | 0 | 6 | 20 |
subtype6 | 1 | 2 | 41 |
P value = 0.082 (Fisher's exact test), Q value = 0.31
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 169 |
subtype1 | 0 | 15 |
subtype2 | 1 | 13 |
subtype3 | 0 | 15 |
subtype4 | 0 | 56 |
subtype5 | 0 | 26 |
subtype6 | 0 | 44 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 60 | 31 | 43 | 33 | 21 |
P value = 0.0151 (logrank test), Q value = 0.075
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 174 | 112 | 0.0 - 94.1 (12.0) |
subtype1 | 58 | 42 | 0.0 - 69.0 (8.1) |
subtype2 | 30 | 15 | 0.0 - 62.0 (18.0) |
subtype3 | 37 | 19 | 1.0 - 82.1 (19.0) |
subtype4 | 30 | 21 | 0.0 - 94.1 (10.0) |
subtype5 | 19 | 15 | 0.0 - 56.1 (9.0) |
P value = 0.000493 (Kruskal-Wallis (anova)), Q value = 0.003
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 188 | 54.9 (16.2) |
subtype1 | 60 | 56.9 (15.1) |
subtype2 | 31 | 56.2 (14.7) |
subtype3 | 43 | 46.7 (15.1) |
subtype4 | 33 | 54.8 (18.7) |
subtype5 | 21 | 64.1 (12.7) |
P value = 0.793 (Fisher's exact test), Q value = 0.95
nPatients | FEMALE | MALE |
---|---|---|
ALL | 87 | 101 |
subtype1 | 26 | 34 |
subtype2 | 12 | 19 |
subtype3 | 22 | 21 |
subtype4 | 17 | 16 |
subtype5 | 10 | 11 |
P value = 0.763 (Fisher's exact test), Q value = 0.95
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 13 | 171 |
subtype1 | 1 | 3 | 56 |
subtype2 | 0 | 1 | 30 |
subtype3 | 1 | 4 | 37 |
subtype4 | 0 | 2 | 30 |
subtype5 | 0 | 3 | 18 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 184 |
subtype1 | 1 | 59 |
subtype2 | 0 | 31 |
subtype3 | 0 | 42 |
subtype4 | 0 | 31 |
subtype5 | 0 | 21 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 70 | 35 | 83 |
P value = 0.161 (logrank test), Q value = 0.44
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 174 | 112 | 0.0 - 94.1 (12.0) |
subtype1 | 68 | 48 | 0.0 - 69.0 (8.1) |
subtype2 | 33 | 19 | 0.0 - 62.0 (12.0) |
subtype3 | 73 | 45 | 0.0 - 94.1 (12.9) |
P value = 0.457 (Kruskal-Wallis (anova)), Q value = 0.76
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 188 | 54.9 (16.2) |
subtype1 | 70 | 55.8 (14.8) |
subtype2 | 35 | 57.3 (15.2) |
subtype3 | 83 | 53.1 (17.6) |
P value = 0.386 (Fisher's exact test), Q value = 0.76
nPatients | FEMALE | MALE |
---|---|---|
ALL | 87 | 101 |
subtype1 | 36 | 34 |
subtype2 | 13 | 22 |
subtype3 | 38 | 45 |
P value = 0.957 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 13 | 171 |
subtype1 | 1 | 6 | 63 |
subtype2 | 0 | 2 | 33 |
subtype3 | 1 | 5 | 75 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 1 | 184 |
subtype1 | 0 | 70 |
subtype2 | 0 | 35 |
subtype3 | 1 | 79 |
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Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/LAML-TB.mergedcluster.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LAML-TB/22506504/LAML-TB.merged_data.txt
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Number of patients = 200
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Number of clustering approaches = 6
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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 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.