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 12 clinical features across 58 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
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 4 subtypes that do not correlate to any clinical features.
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Consensus hierarchical clustering analysis on sequencing-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 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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3 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 |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRseq Mature CNMF subtypes |
MIRseq Mature cHierClus subtypes |
Time to Death | logrank test |
0.264 (1.00) |
0.501 (1.00) |
0.0897 (1.00) |
0.69 (1.00) |
0.778 (1.00) |
0.49 (1.00) |
0.399 (1.00) |
0.49 (1.00) |
AGE | ANOVA |
0.577 (1.00) |
0.462 (1.00) |
0.759 (1.00) |
0.793 (1.00) |
0.799 (1.00) |
0.565 (1.00) |
0.295 (1.00) |
0.587 (1.00) |
NEOPLASM DISEASESTAGE | Chi-square test |
0.199 (1.00) |
0.304 (1.00) |
0.841 (1.00) |
0.461 (1.00) |
0.588 (1.00) |
0.587 (1.00) |
0.73 (1.00) |
0.496 (1.00) |
PATHOLOGY T STAGE | Fisher's exact test |
0.515 (1.00) |
0.192 (1.00) |
0.915 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.6 (1.00) |
0.833 (1.00) |
0.712 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
0.542 (1.00) |
0.919 (1.00) |
0.576 (1.00) |
0.785 (1.00) |
0.53 (1.00) |
0.0668 (1.00) |
0.826 (1.00) |
0.035 (1.00) |
PATHOLOGY M STAGE | Chi-square test |
0.0283 (1.00) |
0.21 (1.00) |
0.0611 (1.00) |
0.0117 (1.00) |
0.413 (1.00) |
0.366 (1.00) |
0.308 (1.00) |
0.246 (1.00) |
GENDER | Fisher's exact test |
0.238 (1.00) |
0.33 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.73 (1.00) |
0.872 (1.00) |
0.917 (1.00) |
HISTOLOGICAL TYPE | Chi-square test |
0.924 (1.00) |
0.622 (1.00) |
0.273 (1.00) |
0.0155 (1.00) |
0.638 (1.00) |
0.311 (1.00) |
0.623 (1.00) |
0.331 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.469 (1.00) |
0.559 (1.00) |
0.706 (1.00) |
0.85 (1.00) |
0.427 (1.00) |
0.979 (1.00) |
0.945 (1.00) |
0.979 (1.00) |
YEAROFTOBACCOSMOKINGONSET | ANOVA |
0.548 (1.00) |
0.284 (1.00) |
0.497 (1.00) |
0.505 (1.00) |
0.908 (1.00) |
0.859 (1.00) |
0.561 (1.00) |
0.859 (1.00) |
COMPLETENESS OF RESECTION | Chi-square test |
0.0162 (1.00) |
0.0149 (1.00) |
0.217 (1.00) |
0.0196 (1.00) |
0.23 (1.00) |
0.298 (1.00) |
0.0889 (1.00) |
0.183 (1.00) |
NUMBER OF LYMPH NODES | ANOVA |
0.293 (1.00) |
0.106 (1.00) |
0.427 (1.00) |
0.392 (1.00) |
0.471 (1.00) |
0.351 (1.00) |
0.623 (1.00) |
0.398 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 11 | 32 | 14 |
P value = 0.264 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 54 | 19 | 0.0 - 49.4 (5.6) |
subtype1 | 10 | 3 | 0.2 - 15.3 (8.0) |
subtype2 | 30 | 10 | 0.1 - 49.4 (6.1) |
subtype3 | 14 | 6 | 0.0 - 19.7 (5.4) |
P value = 0.577 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 66.2 (10.4) |
subtype1 | 11 | 65.4 (9.0) |
subtype2 | 32 | 65.3 (11.2) |
subtype3 | 14 | 68.7 (9.5) |
P value = 0.199 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 3 | 7 | 41 | 2 | 2 |
subtype1 | 0 | 0 | 1 | 8 | 0 | 2 |
subtype2 | 2 | 2 | 5 | 21 | 2 | 0 |
subtype3 | 0 | 1 | 1 | 12 | 0 | 0 |
P value = 0.515 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 6 | 51 |
subtype1 | 0 | 11 |
subtype2 | 5 | 27 |
subtype3 | 1 | 13 |
P value = 0.542 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 14 | 43 |
subtype1 | 2 | 9 |
subtype2 | 10 | 22 |
subtype3 | 2 | 12 |
P value = 0.0283 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 32 | 2 | 23 |
subtype1 | 6 | 2 | 3 |
subtype2 | 16 | 0 | 16 |
subtype3 | 10 | 0 | 4 |
P value = 0.238 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 26 |
subtype1 | 6 | 5 |
subtype2 | 20 | 12 |
subtype3 | 5 | 9 |
P value = 0.924 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 51 | 4 | 1 |
subtype1 | 9 | 1 | 0 |
subtype2 | 29 | 2 | 1 |
subtype3 | 13 | 1 | 0 |
P value = 0.469 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 23.9 (15.9) |
subtype1 | 3 | 30.2 (26.8) |
subtype2 | 7 | 18.4 (13.6) |
subtype3 | 4 | 28.8 (10.3) |
P value = 0.548 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1972.0 (12.8) |
subtype1 | 3 | 1967.0 (15.1) |
subtype2 | 5 | 1970.8 (13.5) |
subtype3 | 3 | 1979.0 (10.6) |
P value = 0.0162 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 32 | 21 | 2 |
subtype1 | 4 | 7 | 0 |
subtype2 | 24 | 6 | 1 |
subtype3 | 4 | 8 | 1 |
P value = 0.293 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 57 | 2.8 (2.8) |
subtype1 | 11 | 2.2 (1.4) |
subtype2 | 32 | 2.5 (3.1) |
subtype3 | 14 | 3.8 (3.1) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 17 | 29 | 12 |
P value = 0.501 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 55 | 19 | 0.0 - 49.4 (5.2) |
subtype1 | 16 | 4 | 0.0 - 15.7 (5.9) |
subtype2 | 27 | 8 | 0.1 - 49.4 (5.2) |
subtype3 | 12 | 7 | 0.3 - 21.9 (5.5) |
P value = 0.462 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 58 | 65.9 (10.4) |
subtype1 | 17 | 63.7 (8.9) |
subtype2 | 29 | 66.2 (10.2) |
subtype3 | 12 | 68.6 (12.8) |
P value = 0.304 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 3 | 7 | 42 | 2 | 2 |
subtype1 | 0 | 0 | 3 | 12 | 0 | 2 |
subtype2 | 2 | 2 | 4 | 20 | 1 | 0 |
subtype3 | 0 | 1 | 0 | 10 | 1 | 0 |
P value = 0.192 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 6 | 52 |
subtype1 | 0 | 17 |
subtype2 | 5 | 24 |
subtype3 | 1 | 11 |
P value = 0.919 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 14 | 44 |
subtype1 | 4 | 13 |
subtype2 | 8 | 21 |
subtype3 | 2 | 10 |
P value = 0.21 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 32 | 2 | 24 |
subtype1 | 9 | 2 | 6 |
subtype2 | 15 | 0 | 14 |
subtype3 | 8 | 0 | 4 |
P value = 0.33 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 31 | 27 |
subtype1 | 10 | 7 |
subtype2 | 17 | 12 |
subtype3 | 4 | 8 |
P value = 0.622 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 52 | 4 | 1 |
subtype1 | 14 | 2 | 0 |
subtype2 | 26 | 2 | 1 |
subtype3 | 12 | 0 | 0 |
P value = 0.559 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 15 | 24.0 (15.3) |
subtype1 | 4 | 18.4 (11.0) |
subtype2 | 8 | 23.9 (18.5) |
subtype3 | 3 | 31.7 (10.4) |
P value = 0.284 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 12 | 1973.2 (13.0) |
subtype1 | 3 | 1980.3 (11.0) |
subtype2 | 6 | 1967.2 (14.0) |
subtype3 | 3 | 1978.3 (9.5) |
P value = 0.0149 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 32 | 21 | 2 |
subtype1 | 6 | 9 | 1 |
subtype2 | 22 | 5 | 0 |
subtype3 | 4 | 7 | 1 |
P value = 0.106 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 58 | 2.7 (2.8) |
subtype1 | 17 | 1.9 (1.5) |
subtype2 | 29 | 2.6 (2.8) |
subtype3 | 12 | 4.2 (3.8) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 17 | 11 | 12 | 10 |
P value = 0.0897 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 16 | 0.0 - 49.4 (4.8) |
subtype1 | 17 | 7 | 0.0 - 19.8 (4.0) |
subtype2 | 11 | 3 | 0.2 - 16.0 (5.2) |
subtype3 | 10 | 5 | 0.1 - 43.8 (6.5) |
subtype4 | 9 | 1 | 0.3 - 49.4 (3.0) |
P value = 0.759 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 50 | 65.3 (10.6) |
subtype1 | 17 | 64.1 (8.4) |
subtype2 | 11 | 63.5 (12.3) |
subtype3 | 12 | 67.5 (11.8) |
subtype4 | 10 | 66.7 (11.5) |
P value = 0.841 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 36 | 2 | 2 |
subtype1 | 0 | 1 | 2 | 13 | 0 | 1 |
subtype2 | 0 | 0 | 1 | 9 | 1 | 0 |
subtype3 | 1 | 1 | 1 | 8 | 1 | 0 |
subtype4 | 1 | 0 | 2 | 6 | 0 | 1 |
P value = 0.915 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 45 |
subtype1 | 1 | 16 |
subtype2 | 1 | 10 |
subtype3 | 2 | 10 |
subtype4 | 1 | 9 |
P value = 0.576 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 38 |
subtype1 | 4 | 13 |
subtype2 | 1 | 10 |
subtype3 | 4 | 8 |
subtype4 | 3 | 7 |
P value = 0.0611 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 26 | 2 | 22 |
subtype1 | 12 | 1 | 4 |
subtype2 | 8 | 0 | 3 |
subtype3 | 4 | 0 | 8 |
subtype4 | 2 | 1 | 7 |
P value = 0.722 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 22 |
subtype1 | 9 | 8 |
subtype2 | 5 | 6 |
subtype3 | 7 | 5 |
subtype4 | 7 | 3 |
P value = 0.273 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 45 | 3 | 1 |
subtype1 | 15 | 1 | 0 |
subtype2 | 11 | 0 | 0 |
subtype3 | 10 | 2 | 0 |
subtype4 | 9 | 0 | 1 |
P value = 0.706 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 13 | 25.0 (16.3) |
subtype1 | 5 | 23.7 (14.4) |
subtype2 | 4 | 28.8 (21.8) |
subtype3 | 2 | 20.5 (27.6) |
subtype4 | 2 | 25.0 (7.1) |
P value = 0.497 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype1 | 4 | 1976.0 (9.0) |
subtype2 | 4 | 1968.8 (17.4) |
subtype3 | 1 | 1968.0 (NA) |
subtype4 | 2 | 1970.5 (14.8) |
P value = 0.217 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 27 | 19 | 1 |
subtype1 | 7 | 9 | 0 |
subtype2 | 5 | 5 | 0 |
subtype3 | 9 | 2 | 0 |
subtype4 | 6 | 3 | 1 |
P value = 0.427 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 50 | 2.8 (2.9) |
subtype1 | 17 | 2.3 (1.6) |
subtype2 | 11 | 3.9 (3.1) |
subtype3 | 12 | 3.0 (4.3) |
subtype4 | 10 | 2.1 (1.8) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 5 | 19 | 26 |
P value = 0.69 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 47 | 16 | 0.0 - 49.4 (4.8) |
subtype1 | 5 | 0 | 0.3 - 12.1 (1.5) |
subtype2 | 18 | 7 | 0.0 - 28.0 (4.9) |
subtype3 | 24 | 9 | 0.1 - 49.4 (5.6) |
P value = 0.793 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 50 | 65.3 (10.6) |
subtype1 | 5 | 68.4 (10.7) |
subtype2 | 19 | 65.1 (8.9) |
subtype3 | 26 | 64.8 (12.0) |
P value = 0.461 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 36 | 2 | 2 |
subtype1 | 1 | 0 | 1 | 3 | 0 | 0 |
subtype2 | 0 | 1 | 2 | 14 | 0 | 2 |
subtype3 | 1 | 1 | 3 | 19 | 2 | 0 |
P value = 0.376 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 45 |
subtype1 | 1 | 4 |
subtype2 | 1 | 18 |
subtype3 | 3 | 23 |
P value = 0.785 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 38 |
subtype1 | 2 | 3 |
subtype2 | 4 | 15 |
subtype3 | 6 | 20 |
P value = 0.0117 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 26 | 2 | 22 |
subtype1 | 0 | 0 | 5 |
subtype2 | 13 | 2 | 4 |
subtype3 | 13 | 0 | 13 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 22 |
subtype1 | 3 | 2 |
subtype2 | 11 | 8 |
subtype3 | 14 | 12 |
P value = 0.0155 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 45 | 3 | 1 |
subtype1 | 3 | 1 | 1 |
subtype2 | 18 | 0 | 0 |
subtype3 | 24 | 2 | 0 |
P value = 0.85 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 13 | 25.0 (16.3) |
subtype2 | 7 | 24.1 (12.1) |
subtype3 | 6 | 26.0 (21.3) |
P value = 0.505 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype2 | 6 | 1974.2 (10.0) |
subtype3 | 5 | 1968.6 (15.1) |
P value = 0.0196 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 27 | 19 | 1 |
subtype1 | 2 | 2 | 1 |
subtype2 | 8 | 10 | 0 |
subtype3 | 17 | 7 | 0 |
P value = 0.392 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 50 | 2.8 (2.9) |
subtype1 | 5 | 1.6 (1.7) |
subtype2 | 19 | 2.4 (1.6) |
subtype3 | 26 | 3.3 (3.6) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 25 | 11 | 17 |
P value = 0.778 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 50 | 17 | 0.0 - 49.4 (4.9) |
subtype1 | 24 | 8 | 0.0 - 28.0 (4.4) |
subtype2 | 11 | 2 | 0.2 - 16.0 (5.2) |
subtype3 | 15 | 7 | 0.1 - 49.4 (6.0) |
P value = 0.799 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 65.9 (10.7) |
subtype1 | 25 | 66.7 (9.7) |
subtype2 | 11 | 64.1 (11.1) |
subtype3 | 17 | 65.9 (12.1) |
P value = 0.588 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 39 | 2 | 2 |
subtype1 | 1 | 1 | 3 | 18 | 0 | 2 |
subtype2 | 0 | 0 | 1 | 10 | 0 | 0 |
subtype3 | 1 | 1 | 2 | 11 | 2 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 48 |
subtype1 | 2 | 23 |
subtype2 | 1 | 10 |
subtype3 | 2 | 15 |
P value = 0.53 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 41 |
subtype1 | 6 | 19 |
subtype2 | 1 | 10 |
subtype3 | 5 | 12 |
P value = 0.413 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 27 | 2 | 24 |
subtype1 | 13 | 2 | 10 |
subtype2 | 7 | 0 | 4 |
subtype3 | 7 | 0 | 10 |
P value = 0.783 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 25 |
subtype1 | 13 | 12 |
subtype2 | 5 | 6 |
subtype3 | 10 | 7 |
P value = 0.638 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 47 | 4 | 1 |
subtype1 | 21 | 2 | 1 |
subtype2 | 11 | 0 | 0 |
subtype3 | 15 | 2 | 0 |
P value = 0.427 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 24.2 (15.8) |
subtype1 | 7 | 24.1 (12.1) |
subtype2 | 4 | 31.5 (18.0) |
subtype3 | 3 | 15.0 (21.7) |
P value = 0.908 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype1 | 6 | 1974.2 (10.0) |
subtype2 | 3 | 1972.7 (19.1) |
subtype3 | 2 | 1962.5 (7.8) |
P value = 0.23 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 20 | 2 |
subtype1 | 10 | 12 | 2 |
subtype2 | 6 | 4 | 0 |
subtype3 | 12 | 4 | 0 |
P value = 0.471 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 2.8 (2.9) |
subtype1 | 25 | 2.4 (1.9) |
subtype2 | 11 | 3.6 (3.2) |
subtype3 | 17 | 2.9 (3.8) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 11 | 19 | 23 |
P value = 0.49 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 50 | 17 | 0.0 - 49.4 (4.9) |
subtype1 | 9 | 5 | 0.1 - 49.4 (7.6) |
subtype2 | 19 | 5 | 0.1 - 19.8 (1.0) |
subtype3 | 22 | 7 | 0.0 - 28.0 (4.4) |
P value = 0.565 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 65.9 (10.7) |
subtype1 | 11 | 65.5 (14.2) |
subtype2 | 19 | 64.1 (9.6) |
subtype3 | 23 | 67.6 (9.8) |
P value = 0.587 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 39 | 2 | 2 |
subtype1 | 1 | 1 | 2 | 7 | 0 | 0 |
subtype2 | 0 | 0 | 1 | 17 | 1 | 0 |
subtype3 | 1 | 1 | 3 | 15 | 1 | 2 |
P value = 0.6 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 48 |
subtype1 | 2 | 9 |
subtype2 | 1 | 18 |
subtype3 | 2 | 21 |
P value = 0.0668 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 41 |
subtype1 | 4 | 7 |
subtype2 | 1 | 18 |
subtype3 | 7 | 16 |
P value = 0.366 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 27 | 2 | 24 |
subtype1 | 4 | 0 | 7 |
subtype2 | 11 | 0 | 8 |
subtype3 | 12 | 2 | 9 |
P value = 0.73 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 25 |
subtype1 | 7 | 4 |
subtype2 | 10 | 9 |
subtype3 | 11 | 12 |
P value = 0.311 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 47 | 4 | 1 |
subtype1 | 9 | 2 | 0 |
subtype2 | 19 | 0 | 0 |
subtype3 | 19 | 2 | 1 |
P value = 0.979 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 24.2 (15.8) |
subtype1 | 2 | 20.5 (27.6) |
subtype2 | 6 | 25.0 (17.9) |
subtype3 | 6 | 24.8 (13.1) |
P value = 0.859 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype1 | 1 | 1968.0 (NA) |
subtype2 | 5 | 1972.8 (17.6) |
subtype3 | 5 | 1971.2 (7.8) |
P value = 0.298 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 20 | 2 |
subtype1 | 8 | 2 | 0 |
subtype2 | 11 | 6 | 1 |
subtype3 | 9 | 12 | 1 |
P value = 0.351 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 2.8 (2.9) |
subtype1 | 11 | 2.8 (4.1) |
subtype2 | 19 | 3.5 (2.9) |
subtype3 | 23 | 2.2 (2.1) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 9 | 23 |
P value = 0.399 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 50 | 17 | 0.0 - 49.4 (4.9) |
subtype1 | 20 | 7 | 0.0 - 28.0 (4.4) |
subtype2 | 9 | 1 | 0.1 - 19.8 (10.0) |
subtype3 | 21 | 9 | 0.1 - 49.4 (5.2) |
P value = 0.295 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 65.9 (10.7) |
subtype1 | 21 | 67.9 (10.1) |
subtype2 | 9 | 61.2 (8.5) |
subtype3 | 23 | 65.9 (11.7) |
P value = 0.73 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 39 | 2 | 2 |
subtype1 | 1 | 1 | 2 | 15 | 0 | 2 |
subtype2 | 0 | 0 | 1 | 8 | 0 | 0 |
subtype3 | 1 | 1 | 3 | 16 | 2 | 0 |
P value = 0.833 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 48 |
subtype1 | 2 | 19 |
subtype2 | 0 | 9 |
subtype3 | 3 | 20 |
P value = 0.826 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 41 |
subtype1 | 5 | 16 |
subtype2 | 1 | 8 |
subtype3 | 6 | 17 |
P value = 0.308 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 27 | 2 | 24 |
subtype1 | 12 | 2 | 7 |
subtype2 | 5 | 0 | 4 |
subtype3 | 10 | 0 | 13 |
P value = 0.872 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 25 |
subtype1 | 10 | 11 |
subtype2 | 5 | 4 |
subtype3 | 13 | 10 |
P value = 0.623 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 47 | 4 | 1 |
subtype1 | 17 | 2 | 1 |
subtype2 | 9 | 0 | 0 |
subtype3 | 21 | 2 | 0 |
P value = 0.945 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 24.2 (15.8) |
subtype1 | 6 | 24.8 (13.1) |
subtype2 | 3 | 21.3 (7.1) |
subtype3 | 5 | 25.4 (23.8) |
P value = 0.561 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype1 | 5 | 1971.2 (7.8) |
subtype2 | 2 | 1984.5 (6.4) |
subtype3 | 4 | 1965.8 (15.8) |
P value = 0.0889 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 20 | 2 |
subtype1 | 7 | 12 | 1 |
subtype2 | 6 | 2 | 1 |
subtype3 | 15 | 6 | 0 |
P value = 0.623 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 2.8 (2.9) |
subtype1 | 21 | 2.4 (2.0) |
subtype2 | 9 | 3.6 (3.5) |
subtype3 | 23 | 2.9 (3.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 22 | 19 |
P value = 0.49 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 50 | 17 | 0.0 - 49.4 (4.9) |
subtype1 | 10 | 5 | 0.1 - 49.4 (6.8) |
subtype2 | 21 | 7 | 0.0 - 28.0 (4.8) |
subtype3 | 19 | 5 | 0.1 - 19.8 (1.0) |
P value = 0.587 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 65.9 (10.7) |
subtype1 | 12 | 65.8 (13.6) |
subtype2 | 22 | 67.5 (10.0) |
subtype3 | 19 | 64.1 (9.6) |
P value = 0.496 (Chi-square test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 2 | 6 | 39 | 2 | 2 |
subtype1 | 1 | 1 | 2 | 7 | 1 | 0 |
subtype2 | 1 | 1 | 3 | 15 | 0 | 2 |
subtype3 | 0 | 0 | 1 | 17 | 1 | 0 |
P value = 0.712 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 5 | 48 |
subtype1 | 2 | 10 |
subtype2 | 2 | 20 |
subtype3 | 1 | 18 |
P value = 0.035 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 12 | 41 |
subtype1 | 5 | 7 |
subtype2 | 6 | 16 |
subtype3 | 1 | 18 |
P value = 0.246 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 27 | 2 | 24 |
subtype1 | 4 | 0 | 8 |
subtype2 | 12 | 2 | 8 |
subtype3 | 11 | 0 | 8 |
P value = 0.917 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 28 | 25 |
subtype1 | 7 | 5 |
subtype2 | 11 | 11 |
subtype3 | 10 | 9 |
P value = 0.331 (Chi-square test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 47 | 4 | 1 |
subtype1 | 10 | 2 | 0 |
subtype2 | 18 | 2 | 1 |
subtype3 | 19 | 0 | 0 |
P value = 0.979 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 14 | 24.2 (15.8) |
subtype1 | 2 | 20.5 (27.6) |
subtype2 | 6 | 24.8 (13.1) |
subtype3 | 6 | 25.0 (17.9) |
P value = 0.859 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 11 | 1971.6 (12.3) |
subtype1 | 1 | 1968.0 (NA) |
subtype2 | 5 | 1971.2 (7.8) |
subtype3 | 5 | 1972.8 (17.6) |
P value = 0.183 (Chi-square test), Q value = 1
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 20 | 2 |
subtype1 | 9 | 2 | 0 |
subtype2 | 8 | 12 | 1 |
subtype3 | 11 | 6 | 1 |
P value = 0.398 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 53 | 2.8 (2.9) |
subtype1 | 12 | 2.6 (4.0) |
subtype2 | 22 | 2.3 (2.1) |
subtype3 | 19 | 3.5 (2.9) |
-
Cluster data file = PAAD-TP.mergedcluster.txt
-
Clinical data file = PAAD-TP.merged_data.txt
-
Number of patients = 58
-
Number of clustering approaches = 8
-
Number of selected clinical features = 12
-
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 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.