(NF1_Any_Mutants cohort)
This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 7 clinical features across 25 patients, one 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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CNMF clustering analysis on RPPA data identified 2 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on RPPA data identified 2 subtypes that correlate to 'AGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that 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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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Chi-square test | Fisher's exact test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.885 (1.00) |
0.654 (1.00) |
0.125 (1.00) |
0.234 (1.00) |
0.577 (1.00) |
0.383 (1.00) |
|
METHLYATION CNMF |
0.483 (1.00) |
0.673 (1.00) |
0.746 (1.00) |
0.0875 (1.00) |
0.666 (1.00) |
0.577 (1.00) |
|
RPPA CNMF subtypes |
0.0334 (1.00) |
0.431 (1.00) |
0.00961 (0.452) |
0.291 (1.00) |
0.0443 (1.00) |
0.195 (1.00) |
|
RPPA cHierClus subtypes |
0.209 (1.00) |
3.9e-05 (0.00187) |
0.0563 (1.00) |
1 (1.00) |
0.0167 (0.77) |
0.166 (1.00) |
|
RNAseq CNMF subtypes |
0.0441 (1.00) |
0.467 (1.00) |
0.42 (1.00) |
0.397 (1.00) |
0.47 (1.00) |
0.482 (1.00) |
|
RNAseq cHierClus subtypes |
0.286 (1.00) |
0.163 (1.00) |
0.0913 (1.00) |
1 (1.00) |
0.336 (1.00) |
0.377 (1.00) |
|
MIRSEQ CNMF |
0.518 (1.00) |
0.373 (1.00) |
0.0835 (1.00) |
1 (1.00) |
0.811 (1.00) |
0.383 (1.00) |
|
MIRSEQ CHIERARCHICAL |
0.132 (1.00) |
0.104 (1.00) |
0.374 (1.00) |
0.145 (1.00) |
0.265 (1.00) |
0.495 (1.00) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 14 |
P value = 0.885 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 16 | 0.2 - 204.6 (27.0) |
subtype1 | 11 | 7 | 10.1 - 96.2 (29.8) |
subtype2 | 14 | 9 | 0.2 - 204.6 (26.7) |
P value = 0.654 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 66.3 (14.3) |
subtype1 | 11 | 64.8 (13.2) |
subtype2 | 14 | 67.4 (15.4) |
P value = 0.125 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 7 | 5 | 13 |
subtype1 | 1 | 2 | 8 |
subtype2 | 6 | 3 | 5 |
P value = 0.234 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 17 |
subtype1 | 2 | 9 |
subtype2 | 6 | 8 |
P value = 0.577 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 16 | 3 | 2 | 2 |
subtype1 | 8 | 1 | 0 | 1 |
subtype2 | 8 | 2 | 2 | 1 |
P value = 0.383 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 3 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype1 | 3 | 0 | 3 | 1 | 1 | 1 | 0 |
subtype2 | 0 | 1 | 3 | 2 | 2 | 3 | 1 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 10 | 15 |
P value = 0.483 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 16 | 0.2 - 204.6 (27.0) |
subtype1 | 10 | 7 | 10.1 - 204.6 (37.7) |
subtype2 | 15 | 9 | 0.2 - 102.0 (26.7) |
P value = 0.673 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 66.3 (14.3) |
subtype1 | 10 | 64.7 (16.0) |
subtype2 | 15 | 67.3 (13.5) |
P value = 0.746 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 7 | 5 | 13 |
subtype1 | 2 | 2 | 6 |
subtype2 | 5 | 3 | 7 |
P value = 0.0875 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 17 |
subtype1 | 1 | 9 |
subtype2 | 7 | 8 |
P value = 0.666 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 16 | 3 | 2 | 2 |
subtype1 | 7 | 1 | 0 | 1 |
subtype2 | 9 | 2 | 2 | 1 |
P value = 0.577 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 3 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype1 | 1 | 1 | 3 | 1 | 0 | 2 | 0 |
subtype2 | 2 | 0 | 3 | 2 | 3 | 2 | 1 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 6 | 15 |
P value = 0.0334 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 15 | 2.6 - 204.6 (27.0) |
subtype1 | 6 | 6 | 14.7 - 68.1 (26.4) |
subtype2 | 15 | 9 | 2.6 - 204.6 (29.8) |
P value = 0.431 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 66.4 (15.4) |
subtype1 | 6 | 71.2 (17.2) |
subtype2 | 15 | 64.5 (14.9) |
P value = 0.00961 (Chi-square test), Q value = 0.45
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 5 | 3 | 13 |
subtype1 | 4 | 1 | 1 |
subtype2 | 1 | 2 | 12 |
P value = 0.291 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 3 | 3 |
subtype2 | 3 | 12 |
P value = 0.0443 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 13 | 3 | 2 | 1 |
subtype1 | 2 | 2 | 2 | 0 |
subtype2 | 11 | 1 | 0 | 1 |
P value = 0.195 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|
ALL | 2 | 1 | 5 | 3 | 3 | 3 |
subtype1 | 0 | 0 | 0 | 1 | 2 | 2 |
subtype2 | 2 | 1 | 5 | 2 | 1 | 1 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 3 | 18 |
P value = 0.209 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 21 | 15 | 2.6 - 204.6 (27.0) |
subtype1 | 3 | 3 | 14.7 - 68.1 (25.9) |
subtype2 | 18 | 12 | 2.6 - 204.6 (27.4) |
P value = 3.9e-05 (t-test), Q value = 0.0019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 66.4 (15.4) |
subtype1 | 3 | 83.3 (2.1) |
subtype2 | 18 | 63.6 (14.9) |
P value = 0.0563 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 5 | 3 | 13 |
subtype1 | 2 | 1 | 0 |
subtype2 | 3 | 2 | 13 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 6 | 15 |
subtype1 | 1 | 2 |
subtype2 | 5 | 13 |
P value = 0.0167 (Chi-square test), Q value = 0.77
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 13 | 3 | 2 | 1 |
subtype1 | 0 | 2 | 1 | 0 |
subtype2 | 13 | 1 | 1 | 1 |
P value = 0.166 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|
ALL | 2 | 1 | 5 | 3 | 3 | 3 |
subtype1 | 0 | 0 | 0 | 0 | 1 | 2 |
subtype2 | 2 | 1 | 5 | 3 | 2 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 9 | 11 |
P value = 0.0441 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 16 | 0.2 - 204.6 (27.0) |
subtype1 | 5 | 3 | 20.9 - 204.6 (102.0) |
subtype2 | 9 | 5 | 10.1 - 96.2 (33.7) |
subtype3 | 11 | 8 | 0.2 - 68.1 (25.9) |
P value = 0.467 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 66.3 (14.3) |
subtype1 | 5 | 59.6 (14.5) |
subtype2 | 9 | 66.2 (14.2) |
subtype3 | 11 | 69.4 (14.5) |
P value = 0.42 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 7 | 5 | 13 |
subtype1 | 2 | 1 | 2 |
subtype2 | 1 | 1 | 7 |
subtype3 | 4 | 3 | 4 |
P value = 0.397 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 17 |
subtype1 | 3 | 2 |
subtype2 | 2 | 7 |
subtype3 | 3 | 8 |
P value = 0.47 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 16 | 3 | 2 | 2 |
subtype1 | 3 | 0 | 1 | 0 |
subtype2 | 7 | 1 | 0 | 0 |
subtype3 | 6 | 2 | 1 | 2 |
P value = 0.482 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 3 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype1 | 0 | 0 | 2 | 1 | 1 | 0 | 0 |
subtype2 | 2 | 0 | 3 | 1 | 1 | 0 | 0 |
subtype3 | 1 | 1 | 1 | 1 | 1 | 4 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 4 | 7 | 6 | 8 |
P value = 0.286 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 16 | 0.2 - 204.6 (27.0) |
subtype1 | 4 | 3 | 10.1 - 204.6 (38.2) |
subtype2 | 7 | 4 | 18.6 - 96.2 (33.7) |
subtype3 | 6 | 5 | 0.2 - 68.1 (23.1) |
subtype4 | 8 | 4 | 2.6 - 136.4 (26.7) |
P value = 0.163 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 66.3 (14.3) |
subtype1 | 4 | 51.8 (14.9) |
subtype2 | 7 | 68.1 (13.4) |
subtype3 | 6 | 71.0 (13.9) |
subtype4 | 8 | 68.4 (12.9) |
P value = 0.0913 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 7 | 5 | 13 |
subtype1 | 2 | 1 | 1 |
subtype2 | 0 | 0 | 7 |
subtype3 | 3 | 2 | 1 |
subtype4 | 2 | 2 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 17 |
subtype1 | 1 | 3 |
subtype2 | 2 | 5 |
subtype3 | 2 | 4 |
subtype4 | 3 | 5 |
P value = 0.336 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 16 | 3 | 2 | 2 |
subtype1 | 2 | 0 | 1 | 0 |
subtype2 | 6 | 1 | 0 | 0 |
subtype3 | 2 | 2 | 1 | 1 |
subtype4 | 6 | 0 | 0 | 1 |
P value = 0.377 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 3 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 |
subtype2 | 1 | 0 | 3 | 1 | 1 | 0 | 0 |
subtype3 | 1 | 0 | 0 | 0 | 1 | 3 | 1 |
subtype4 | 0 | 1 | 3 | 1 | 0 | 1 | 0 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 11 | 14 |
P value = 0.518 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 25 | 16 | 0.2 - 204.6 (27.0) |
subtype1 | 11 | 8 | 0.2 - 204.6 (25.9) |
subtype2 | 14 | 8 | 2.6 - 136.4 (30.4) |
P value = 0.373 (t-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 66.3 (14.3) |
subtype1 | 11 | 63.3 (15.6) |
subtype2 | 14 | 68.6 (13.3) |
P value = 0.0835 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 7 | 5 | 13 |
subtype1 | 5 | 3 | 3 |
subtype2 | 2 | 2 | 10 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 17 |
subtype1 | 4 | 7 |
subtype2 | 4 | 10 |
P value = 0.811 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 16 | 3 | 2 | 2 |
subtype1 | 6 | 2 | 1 | 1 |
subtype2 | 10 | 1 | 1 | 1 |
P value = 0.383 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 3 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype1 | 2 | 0 | 1 | 1 | 1 | 3 | 1 |
subtype2 | 1 | 1 | 5 | 2 | 2 | 1 | 0 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 1 | 4 | 2 | 4 | 8 | 6 |
P value = 0.132 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 22 | 14 | 0.2 - 204.6 (26.9) |
subtype2 | 4 | 3 | 10.1 - 204.6 (64.8) |
subtype4 | 4 | 2 | 0.2 - 24.4 (17.5) |
subtype5 | 8 | 6 | 2.6 - 74.7 (26.9) |
subtype6 | 6 | 3 | 14.3 - 136.4 (54.8) |
P value = 0.104 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 22 | 66.0 (14.7) |
subtype2 | 4 | 49.8 (10.9) |
subtype4 | 4 | 69.2 (11.0) |
subtype5 | 8 | 69.2 (14.1) |
subtype6 | 6 | 70.2 (15.1) |
P value = 0.374 (Chi-square test), Q value = 1
nPatients | DISTANT METASTASIS | REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | REGIONAL LYMPH NODE |
---|---|---|---|
ALL | 6 | 5 | 11 |
subtype2 | 1 | 2 | 1 |
subtype4 | 2 | 1 | 1 |
subtype5 | 2 | 0 | 6 |
subtype6 | 1 | 2 | 3 |
P value = 0.145 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 8 | 14 |
subtype2 | 2 | 2 |
subtype4 | 2 | 2 |
subtype5 | 4 | 4 |
subtype6 | 0 | 6 |
P value = 0.265 (Chi-square test), Q value = 1
nPatients | N0 | N1B | N2C | N3 |
---|---|---|---|---|
ALL | 13 | 3 | 2 | 2 |
subtype2 | 2 | 0 | 1 | 0 |
subtype4 | 1 | 2 | 0 | 1 |
subtype5 | 6 | 0 | 0 | 1 |
subtype6 | 4 | 1 | 1 | 0 |
P value = 0.495 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE II | STAGE IIB | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|
ALL | 1 | 1 | 6 | 3 | 3 | 4 | 1 |
subtype2 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
subtype4 | 0 | 0 | 0 | 0 | 1 | 2 | 1 |
subtype5 | 1 | 0 | 2 | 2 | 0 | 1 | 0 |
subtype6 | 0 | 1 | 3 | 0 | 1 | 1 | 0 |
-
Cluster data file = SKCM-NF1_Any_Mutants.mergedcluster.txt
-
Clinical data file = SKCM-NF1_Any_Mutants.clin.merged.picked.txt
-
Number of patients = 25
-
Number of clustering approaches = 8
-
Number of selected clinical features = 7
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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 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 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 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.