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 93 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
-
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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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 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 6 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
6 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 |
0.0488 (1.00) |
0.082 (1.00) |
0.0438 (1.00) |
0.393 (1.00) |
0.408 (1.00) |
0.118 (1.00) |
0.625 (1.00) |
0.0439 (1.00) |
AGE | Kruskal-Wallis (anova) |
0.939 (1.00) |
0.323 (1.00) |
0.614 (1.00) |
0.981 (1.00) |
0.863 (1.00) |
0.522 (1.00) |
0.704 (1.00) |
0.798 (1.00) |
NEOPLASM DISEASESTAGE | Fisher's exact test |
0.256 (1.00) |
0.665 (1.00) |
0.103 (1.00) |
0.165 (1.00) |
0.218 (1.00) |
0.754 (1.00) |
0.145 (1.00) |
0.0881 (1.00) |
PATHOLOGY T STAGE | Fisher's exact test |
0.499 (1.00) |
0.182 (1.00) |
0.0666 (1.00) |
0.128 (1.00) |
0.0301 (1.00) |
0.342 (1.00) |
0.584 (1.00) |
0.135 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
0.443 (1.00) |
0.953 (1.00) |
0.167 (1.00) |
0.0251 (1.00) |
0.359 (1.00) |
0.195 (1.00) |
0.947 (1.00) |
0.0326 (1.00) |
PATHOLOGY M STAGE | Fisher's exact test |
0.0893 (1.00) |
0.632 (1.00) |
0.528 (1.00) |
0.0472 (1.00) |
0.907 (1.00) |
0.268 (1.00) |
0.582 (1.00) |
0.878 (1.00) |
GENDER | Fisher's exact test |
0.524 (1.00) |
0.228 (1.00) |
0.962 (1.00) |
0.193 (1.00) |
0.636 (1.00) |
0.597 (1.00) |
0.727 (1.00) |
0.919 (1.00) |
HISTOLOGICAL TYPE | Fisher's exact test |
0.846 (1.00) |
1 (1.00) |
0.478 (1.00) |
2e-05 (0.00192) |
0.186 (1.00) |
0.068 (1.00) |
0.844 (1.00) |
0.115 (1.00) |
NUMBERPACKYEARSSMOKED | Kruskal-Wallis (anova) |
0.106 (1.00) |
0.0705 (1.00) |
0.428 (1.00) |
0.31 (1.00) |
0.479 (1.00) |
0.749 (1.00) |
0.214 (1.00) |
0.331 (1.00) |
COMPLETENESS OF RESECTION | Fisher's exact test |
0.0437 (1.00) |
0.18 (1.00) |
0.028 (1.00) |
0.055 (1.00) |
0.0544 (1.00) |
0.134 (1.00) |
0.0405 (1.00) |
0.182 (1.00) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.228 (1.00) |
0.841 (1.00) |
0.182 (1.00) |
0.0314 (1.00) |
0.558 (1.00) |
0.189 (1.00) |
0.799 (1.00) |
0.064 (1.00) |
RACE | Fisher's exact test |
0.669 (1.00) |
0.654 (1.00) |
0.881 (1.00) |
0.962 (1.00) |
0.799 (1.00) |
0.464 (1.00) |
0.524 (1.00) |
0.184 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 23 | 43 | 14 | 6 |
P value = 0.0488 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 61 | 11 | 1.0 - 1991.0 (181.0) |
subtype1 | 16 | 3 | 4.0 - 1991.0 (430.5) |
subtype2 | 32 | 6 | 3.0 - 1989.0 (63.0) |
subtype3 | 9 | 2 | 1.0 - 396.0 (110.0) |
subtype4 | 4 | 0 | 127.0 - 392.0 (230.0) |
P value = 0.939 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 86 | 65.7 (10.7) |
subtype1 | 23 | 64.5 (11.0) |
subtype2 | 43 | 66.1 (11.1) |
subtype3 | 14 | 65.9 (10.7) |
subtype4 | 6 | 66.8 (8.9) |
P value = 0.256 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 4 | 14 | 61 | 2 | 3 |
subtype1 | 0 | 1 | 2 | 20 | 0 | 0 |
subtype2 | 2 | 3 | 8 | 28 | 2 | 0 |
subtype3 | 0 | 0 | 3 | 8 | 0 | 3 |
subtype4 | 0 | 0 | 1 | 5 | 0 | 0 |
P value = 0.499 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 78 |
subtype1 | 2 | 21 |
subtype2 | 6 | 37 |
subtype3 | 0 | 14 |
subtype4 | 0 | 6 |
P value = 0.443 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 21 | 64 |
subtype1 | 3 | 20 |
subtype2 | 13 | 29 |
subtype3 | 4 | 10 |
subtype4 | 1 | 5 |
P value = 0.0893 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 41 | 3 | 42 |
subtype1 | 13 | 0 | 10 |
subtype2 | 20 | 0 | 23 |
subtype3 | 5 | 3 | 6 |
subtype4 | 3 | 0 | 3 |
P value = 0.524 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 42 |
subtype1 | 9 | 14 |
subtype2 | 25 | 18 |
subtype3 | 7 | 7 |
subtype4 | 3 | 3 |
P value = 0.846 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 74 | 8 | 3 |
subtype1 | 20 | 1 | 1 |
subtype2 | 37 | 4 | 2 |
subtype3 | 12 | 2 | 0 |
subtype4 | 5 | 1 | 0 |
P value = 0.106 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 26 | 25.3 (15.3) |
subtype1 | 6 | 37.8 (11.1) |
subtype2 | 12 | 20.8 (15.8) |
subtype3 | 5 | 23.6 (12.2) |
subtype4 | 3 | 21.2 (18.3) |
P value = 0.0437 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 55 | 25 | 1 | 2 |
subtype1 | 12 | 8 | 1 | 1 |
subtype2 | 34 | 7 | 0 | 1 |
subtype3 | 7 | 6 | 0 | 0 |
subtype4 | 2 | 4 | 0 | 0 |
P value = 0.228 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 85 | 2.7 (2.9) |
subtype1 | 23 | 3.7 (3.7) |
subtype2 | 42 | 2.4 (2.8) |
subtype3 | 14 | 1.9 (1.4) |
subtype4 | 6 | 3.0 (2.4) |
P value = 0.669 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 6 | 74 |
subtype1 | 1 | 1 | 19 |
subtype2 | 1 | 4 | 36 |
subtype3 | 0 | 0 | 14 |
subtype4 | 0 | 1 | 5 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 26 | 24 |
P value = 0.082 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 67 | 11 | 1.0 - 1991.0 (181.0) |
subtype1 | 30 | 5 | 1.0 - 1991.0 (218.5) |
subtype2 | 21 | 4 | 3.0 - 1955.0 (91.0) |
subtype3 | 16 | 2 | 4.0 - 851.0 (180.0) |
P value = 0.323 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 93 | 66.1 (10.7) |
subtype1 | 43 | 65.7 (10.1) |
subtype2 | 26 | 69.0 (10.0) |
subtype3 | 24 | 63.5 (12.0) |
P value = 0.665 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 5 | 15 | 66 | 2 | 3 |
subtype1 | 0 | 2 | 7 | 32 | 0 | 2 |
subtype2 | 2 | 1 | 4 | 17 | 1 | 1 |
subtype3 | 0 | 2 | 4 | 17 | 1 | 0 |
P value = 0.182 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 9 | 84 |
subtype1 | 2 | 41 |
subtype2 | 5 | 21 |
subtype3 | 2 | 22 |
P value = 0.953 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 23 | 69 |
subtype1 | 10 | 33 |
subtype2 | 7 | 19 |
subtype3 | 6 | 17 |
P value = 0.632 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 43 | 3 | 47 |
subtype1 | 19 | 2 | 22 |
subtype2 | 10 | 1 | 15 |
subtype3 | 14 | 0 | 10 |
P value = 0.228 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 46 | 47 |
subtype1 | 17 | 26 |
subtype2 | 15 | 11 |
subtype3 | 14 | 10 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 81 | 8 | 3 |
subtype1 | 37 | 4 | 1 |
subtype2 | 23 | 2 | 1 |
subtype3 | 21 | 2 | 1 |
P value = 0.0705 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 31 | 25.3 (16.1) |
subtype1 | 17 | 29.9 (15.5) |
subtype2 | 7 | 15.3 (20.4) |
subtype3 | 7 | 24.0 (8.3) |
P value = 0.18 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 58 | 28 | 1 | 2 |
subtype1 | 21 | 17 | 1 | 2 |
subtype2 | 18 | 6 | 0 | 0 |
subtype3 | 19 | 5 | 0 | 0 |
P value = 0.841 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 92 | 2.6 (2.9) |
subtype1 | 43 | 2.7 (2.9) |
subtype2 | 26 | 2.4 (2.8) |
subtype3 | 23 | 2.7 (3.1) |
P value = 0.654 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 6 | 81 |
subtype1 | 0 | 3 | 39 |
subtype2 | 1 | 2 | 22 |
subtype3 | 1 | 1 | 20 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 43 | 24 | 22 |
P value = 0.0438 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 66 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 35 | 4 | 4.0 - 1991.0 (197.0) |
subtype2 | 19 | 5 | 1.0 - 1989.0 (300.0) |
subtype3 | 12 | 2 | 3.0 - 449.0 (26.5) |
P value = 0.614 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 66.0 (10.7) |
subtype1 | 43 | 65.0 (10.8) |
subtype2 | 24 | 67.5 (10.2) |
subtype3 | 22 | 66.5 (11.1) |
P value = 0.103 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 5 | 14 | 64 | 2 | 2 |
subtype1 | 1 | 1 | 9 | 30 | 0 | 2 |
subtype2 | 0 | 0 | 3 | 20 | 1 | 0 |
subtype3 | 1 | 4 | 2 | 14 | 1 | 0 |
P value = 0.0666 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 9 | 80 |
subtype1 | 2 | 41 |
subtype2 | 2 | 22 |
subtype3 | 5 | 17 |
P value = 0.167 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 66 |
subtype1 | 11 | 31 |
subtype2 | 3 | 21 |
subtype3 | 8 | 14 |
P value = 0.528 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 41 | 2 | 46 |
subtype1 | 18 | 2 | 23 |
subtype2 | 14 | 0 | 10 |
subtype3 | 9 | 0 | 13 |
P value = 0.962 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 44 |
subtype1 | 21 | 22 |
subtype2 | 13 | 11 |
subtype3 | 11 | 11 |
P value = 0.478 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 77 | 8 | 3 |
subtype1 | 34 | 5 | 3 |
subtype2 | 23 | 1 | 0 |
subtype3 | 20 | 2 | 0 |
P value = 0.428 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 26.1 (15.7) |
subtype1 | 17 | 29.5 (14.7) |
subtype2 | 10 | 21.6 (16.7) |
subtype3 | 3 | 21.7 (19.6) |
P value = 0.028 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 54 | 28 | 1 | 2 |
subtype1 | 21 | 17 | 1 | 2 |
subtype2 | 14 | 9 | 0 | 0 |
subtype3 | 19 | 2 | 0 | 0 |
P value = 0.182 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 88 | 2.7 (2.9) |
subtype1 | 42 | 2.2 (2.0) |
subtype2 | 24 | 3.7 (3.7) |
subtype3 | 22 | 2.6 (3.5) |
P value = 0.881 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 78 |
subtype1 | 1 | 2 | 39 |
subtype2 | 1 | 2 | 20 |
subtype3 | 0 | 1 | 19 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 23 | 12 | 13 | 13 | 21 | 7 |
P value = 0.393 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 66 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 15 | 2 | 5.0 - 1991.0 (197.0) |
subtype2 | 9 | 4 | 4.0 - 1989.0 (300.0) |
subtype3 | 5 | 1 | 3.0 - 449.0 (8.0) |
subtype4 | 12 | 1 | 7.0 - 844.0 (203.0) |
subtype5 | 18 | 3 | 1.0 - 1968.0 (32.0) |
subtype6 | 7 | 0 | 8.0 - 416.0 (194.0) |
P value = 0.981 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 89 | 66.0 (10.7) |
subtype1 | 23 | 66.1 (11.4) |
subtype2 | 12 | 66.9 (11.8) |
subtype3 | 13 | 64.5 (12.3) |
subtype4 | 13 | 67.3 (11.1) |
subtype5 | 21 | 66.3 (9.8) |
subtype6 | 7 | 64.0 (7.3) |
P value = 0.165 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 5 | 14 | 64 | 2 | 2 |
subtype1 | 0 | 1 | 4 | 17 | 0 | 1 |
subtype2 | 0 | 0 | 2 | 10 | 0 | 0 |
subtype3 | 1 | 3 | 2 | 6 | 1 | 0 |
subtype4 | 1 | 1 | 4 | 6 | 0 | 1 |
subtype5 | 0 | 0 | 2 | 18 | 1 | 0 |
subtype6 | 0 | 0 | 0 | 7 | 0 | 0 |
P value = 0.128 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 9 | 80 |
subtype1 | 1 | 22 |
subtype2 | 0 | 12 |
subtype3 | 4 | 9 |
subtype4 | 2 | 11 |
subtype5 | 2 | 19 |
subtype6 | 0 | 7 |
P value = 0.0251 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 66 |
subtype1 | 6 | 17 |
subtype2 | 2 | 10 |
subtype3 | 7 | 6 |
subtype4 | 5 | 7 |
subtype5 | 2 | 19 |
subtype6 | 0 | 7 |
P value = 0.0472 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 41 | 2 | 46 |
subtype1 | 14 | 1 | 8 |
subtype2 | 6 | 0 | 6 |
subtype3 | 6 | 0 | 7 |
subtype4 | 1 | 1 | 11 |
subtype5 | 12 | 0 | 9 |
subtype6 | 2 | 0 | 5 |
P value = 0.193 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 45 | 44 |
subtype1 | 13 | 10 |
subtype2 | 8 | 4 |
subtype3 | 8 | 5 |
subtype4 | 3 | 10 |
subtype5 | 11 | 10 |
subtype6 | 2 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0019
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 77 | 8 | 3 |
subtype1 | 22 | 0 | 0 |
subtype2 | 11 | 1 | 0 |
subtype3 | 12 | 1 | 0 |
subtype4 | 5 | 5 | 3 |
subtype5 | 21 | 0 | 0 |
subtype6 | 6 | 1 | 0 |
P value = 0.31 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 26.1 (15.7) |
subtype1 | 9 | 32.4 (18.3) |
subtype2 | 6 | 29.8 (19.0) |
subtype3 | 2 | 32.0 (11.3) |
subtype4 | 5 | 24.0 (6.5) |
subtype5 | 7 | 16.2 (13.1) |
subtype6 | 1 | 15.0 (NA) |
P value = 0.055 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 54 | 28 | 1 | 2 |
subtype1 | 10 | 10 | 1 | 0 |
subtype2 | 5 | 6 | 0 | 0 |
subtype3 | 12 | 1 | 0 | 0 |
subtype4 | 8 | 3 | 0 | 2 |
subtype5 | 13 | 7 | 0 | 0 |
subtype6 | 6 | 1 | 0 | 0 |
P value = 0.0314 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 88 | 2.7 (2.9) |
subtype1 | 23 | 2.6 (2.3) |
subtype2 | 12 | 2.3 (1.5) |
subtype3 | 13 | 2.3 (4.0) |
subtype4 | 12 | 1.0 (1.0) |
subtype5 | 21 | 4.1 (4.0) |
subtype6 | 7 | 2.9 (1.2) |
P value = 0.962 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 78 |
subtype1 | 0 | 1 | 20 |
subtype2 | 0 | 0 | 11 |
subtype3 | 0 | 1 | 11 |
subtype4 | 1 | 1 | 11 |
subtype5 | 1 | 2 | 18 |
subtype6 | 0 | 0 | 7 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 29 | 23 | 13 | 19 |
P value = 0.408 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 62 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 22 | 4 | 1.0 - 1991.0 (297.0) |
subtype2 | 21 | 5 | 4.0 - 1989.0 (295.0) |
subtype3 | 6 | 1 | 3.0 - 329.0 (177.0) |
subtype4 | 13 | 1 | 4.0 - 851.0 (91.0) |
P value = 0.863 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.5 (10.7) |
subtype1 | 29 | 64.6 (10.6) |
subtype2 | 23 | 66.0 (9.5) |
subtype3 | 13 | 67.3 (11.7) |
subtype4 | 19 | 64.9 (12.1) |
P value = 0.218 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 4 | 13 | 61 | 2 | 2 |
subtype1 | 0 | 0 | 6 | 21 | 0 | 2 |
subtype2 | 0 | 0 | 3 | 19 | 1 | 0 |
subtype3 | 1 | 2 | 2 | 8 | 0 | 0 |
subtype4 | 1 | 2 | 2 | 13 | 1 | 0 |
P value = 0.0301 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 76 |
subtype1 | 0 | 29 |
subtype2 | 2 | 21 |
subtype3 | 3 | 10 |
subtype4 | 3 | 16 |
P value = 0.359 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 20 | 63 |
subtype1 | 7 | 22 |
subtype2 | 3 | 20 |
subtype3 | 5 | 8 |
subtype4 | 5 | 13 |
P value = 0.907 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 39 | 2 | 43 |
subtype1 | 12 | 2 | 15 |
subtype2 | 12 | 0 | 11 |
subtype3 | 6 | 0 | 7 |
subtype4 | 9 | 0 | 10 |
P value = 0.636 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 40 |
subtype1 | 17 | 12 |
subtype2 | 13 | 10 |
subtype3 | 5 | 8 |
subtype4 | 9 | 10 |
P value = 0.186 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 72 | 8 | 3 |
subtype1 | 23 | 4 | 1 |
subtype2 | 23 | 0 | 0 |
subtype3 | 11 | 2 | 0 |
subtype4 | 15 | 2 | 2 |
P value = 0.479 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 25.3 (15.0) |
subtype1 | 13 | 28.8 (14.9) |
subtype2 | 8 | 23.6 (17.2) |
subtype3 | 1 | 1.0 (NA) |
subtype4 | 5 | 23.8 (9.6) |
P value = 0.0544 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 52 | 25 | 1 | 2 |
subtype1 | 13 | 13 | 0 | 1 |
subtype2 | 14 | 8 | 0 | 0 |
subtype3 | 10 | 2 | 0 | 0 |
subtype4 | 15 | 2 | 1 | 1 |
P value = 0.558 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 83 | 2.7 (3.0) |
subtype1 | 29 | 2.2 (1.7) |
subtype2 | 23 | 3.5 (3.7) |
subtype3 | 13 | 2.9 (4.2) |
subtype4 | 18 | 2.4 (2.3) |
P value = 0.799 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 73 |
subtype1 | 0 | 1 | 27 |
subtype2 | 1 | 2 | 19 |
subtype3 | 0 | 1 | 11 |
subtype4 | 1 | 1 | 16 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 15 | 19 | 17 | 6 | 16 | 11 |
P value = 0.118 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 62 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 9 | 2 | 110.0 - 1991.0 (181.0) |
subtype2 | 16 | 2 | 8.0 - 1951.0 (97.5) |
subtype3 | 9 | 2 | 3.0 - 449.0 (19.0) |
subtype4 | 6 | 2 | 1.0 - 1968.0 (23.0) |
subtype5 | 13 | 2 | 8.0 - 1975.0 (369.0) |
subtype6 | 9 | 1 | 5.0 - 1989.0 (160.0) |
P value = 0.522 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.5 (10.7) |
subtype1 | 15 | 66.8 (10.3) |
subtype2 | 19 | 63.4 (10.2) |
subtype3 | 17 | 67.6 (12.6) |
subtype4 | 6 | 69.0 (6.7) |
subtype5 | 16 | 65.8 (11.1) |
subtype6 | 11 | 61.6 (10.4) |
P value = 0.754 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 4 | 13 | 61 | 2 | 2 |
subtype1 | 0 | 1 | 2 | 12 | 0 | 0 |
subtype2 | 0 | 0 | 2 | 16 | 1 | 0 |
subtype3 | 1 | 3 | 2 | 10 | 1 | 0 |
subtype4 | 0 | 0 | 1 | 5 | 0 | 0 |
subtype5 | 1 | 0 | 4 | 10 | 0 | 1 |
subtype6 | 0 | 0 | 2 | 8 | 0 | 1 |
P value = 0.342 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 76 |
subtype1 | 1 | 14 |
subtype2 | 1 | 18 |
subtype3 | 4 | 13 |
subtype4 | 1 | 5 |
subtype5 | 1 | 15 |
subtype6 | 0 | 11 |
P value = 0.195 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 20 | 63 |
subtype1 | 3 | 12 |
subtype2 | 1 | 17 |
subtype3 | 7 | 10 |
subtype4 | 1 | 5 |
subtype5 | 5 | 11 |
subtype6 | 3 | 8 |
P value = 0.268 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 39 | 2 | 43 |
subtype1 | 10 | 0 | 5 |
subtype2 | 11 | 0 | 8 |
subtype3 | 7 | 0 | 10 |
subtype4 | 2 | 0 | 4 |
subtype5 | 4 | 1 | 11 |
subtype6 | 5 | 1 | 5 |
P value = 0.597 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 40 |
subtype1 | 7 | 8 |
subtype2 | 8 | 11 |
subtype3 | 9 | 8 |
subtype4 | 5 | 1 |
subtype5 | 8 | 8 |
subtype6 | 7 | 4 |
P value = 0.068 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 72 | 8 | 3 |
subtype1 | 14 | 0 | 0 |
subtype2 | 18 | 0 | 1 |
subtype3 | 14 | 3 | 0 |
subtype4 | 6 | 0 | 0 |
subtype5 | 10 | 4 | 2 |
subtype6 | 10 | 1 | 0 |
P value = 0.749 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 25.3 (15.0) |
subtype1 | 6 | 31.9 (18.0) |
subtype2 | 6 | 25.0 (17.9) |
subtype3 | 3 | 21.7 (19.6) |
subtype4 | 3 | 13.5 (17.6) |
subtype5 | 5 | 26.0 (8.2) |
subtype6 | 4 | 26.5 (9.4) |
P value = 0.134 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 52 | 25 | 1 | 2 |
subtype1 | 9 | 4 | 1 | 0 |
subtype2 | 11 | 6 | 0 | 1 |
subtype3 | 14 | 2 | 0 | 0 |
subtype4 | 5 | 1 | 0 | 0 |
subtype5 | 10 | 5 | 0 | 1 |
subtype6 | 3 | 7 | 0 | 0 |
P value = 0.189 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 83 | 2.7 (3.0) |
subtype1 | 15 | 3.1 (2.5) |
subtype2 | 18 | 3.6 (3.0) |
subtype3 | 17 | 2.3 (3.5) |
subtype4 | 6 | 4.8 (5.7) |
subtype5 | 16 | 1.7 (1.4) |
subtype6 | 11 | 2.0 (1.4) |
P value = 0.464 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 73 |
subtype1 | 0 | 1 | 13 |
subtype2 | 2 | 2 | 14 |
subtype3 | 0 | 1 | 15 |
subtype4 | 0 | 1 | 5 |
subtype5 | 0 | 0 | 15 |
subtype6 | 0 | 0 | 11 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 33 | 21 | 30 |
P value = 0.625 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 62 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 25 | 5 | 1.0 - 1991.0 (347.0) |
subtype2 | 20 | 5 | 3.0 - 1989.0 (264.0) |
subtype3 | 17 | 1 | 4.0 - 851.0 (29.0) |
P value = 0.704 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.5 (10.7) |
subtype1 | 33 | 66.3 (11.0) |
subtype2 | 21 | 64.3 (10.3) |
subtype3 | 30 | 65.4 (10.9) |
P value = 0.145 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 4 | 13 | 61 | 2 | 2 |
subtype1 | 1 | 0 | 5 | 25 | 0 | 2 |
subtype2 | 1 | 0 | 4 | 16 | 0 | 0 |
subtype3 | 0 | 4 | 4 | 20 | 2 | 0 |
P value = 0.584 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 76 |
subtype1 | 2 | 31 |
subtype2 | 2 | 19 |
subtype3 | 4 | 26 |
P value = 0.947 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 20 | 63 |
subtype1 | 7 | 26 |
subtype2 | 5 | 16 |
subtype3 | 8 | 21 |
P value = 0.582 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 39 | 2 | 43 |
subtype1 | 13 | 2 | 18 |
subtype2 | 10 | 0 | 11 |
subtype3 | 16 | 0 | 14 |
P value = 0.727 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 40 |
subtype1 | 18 | 15 |
subtype2 | 12 | 9 |
subtype3 | 14 | 16 |
P value = 0.844 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 72 | 8 | 3 |
subtype1 | 26 | 4 | 2 |
subtype2 | 19 | 2 | 0 |
subtype3 | 27 | 2 | 1 |
P value = 0.214 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 25.3 (15.0) |
subtype1 | 14 | 29.2 (14.3) |
subtype2 | 7 | 21.7 (18.6) |
subtype3 | 6 | 20.5 (11.8) |
P value = 0.0405 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 52 | 25 | 1 | 2 |
subtype1 | 16 | 13 | 1 | 1 |
subtype2 | 11 | 8 | 0 | 0 |
subtype3 | 25 | 4 | 0 | 1 |
P value = 0.799 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 83 | 2.7 (3.0) |
subtype1 | 33 | 2.8 (3.1) |
subtype2 | 21 | 2.4 (2.7) |
subtype3 | 29 | 2.8 (3.1) |
P value = 0.524 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 73 |
subtype1 | 0 | 1 | 31 |
subtype2 | 1 | 2 | 17 |
subtype3 | 1 | 2 | 25 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 41 | 25 | 18 |
P value = 0.0439 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Year | |
---|---|---|---|
ALL | 62 | 11 | 1.0 - 1991.0 (187.5) |
subtype1 | 30 | 4 | 5.0 - 1991.0 (273.5) |
subtype2 | 22 | 5 | 1.0 - 1989.0 (32.0) |
subtype3 | 10 | 2 | 3.0 - 449.0 (92.5) |
P value = 0.798 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 84 | 65.5 (10.7) |
subtype1 | 41 | 65.1 (10.7) |
subtype2 | 25 | 65.4 (9.0) |
subtype3 | 18 | 66.5 (13.0) |
P value = 0.0881 (Fisher's exact test), Q value = 1
nPatients | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IV |
---|---|---|---|---|---|---|
ALL | 2 | 4 | 13 | 61 | 2 | 2 |
subtype1 | 1 | 1 | 8 | 29 | 0 | 2 |
subtype2 | 0 | 0 | 2 | 22 | 1 | 0 |
subtype3 | 1 | 3 | 3 | 10 | 1 | 0 |
P value = 0.135 (Fisher's exact test), Q value = 1
nPatients | T1+T2 | T3+T4 |
---|---|---|
ALL | 8 | 76 |
subtype1 | 2 | 39 |
subtype2 | 2 | 23 |
subtype3 | 4 | 14 |
P value = 0.0326 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 20 | 63 |
subtype1 | 11 | 30 |
subtype2 | 2 | 23 |
subtype3 | 7 | 10 |
P value = 0.878 (Fisher's exact test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 39 | 2 | 43 |
subtype1 | 18 | 2 | 21 |
subtype2 | 13 | 0 | 12 |
subtype3 | 8 | 0 | 10 |
P value = 0.919 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 44 | 40 |
subtype1 | 21 | 20 |
subtype2 | 14 | 11 |
subtype3 | 9 | 9 |
P value = 0.115 (Fisher's exact test), Q value = 1
nPatients | PANCREAS-ADENOCARCINOMA DUCTAL TYPE | PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA |
---|---|---|---|
ALL | 72 | 8 | 3 |
subtype1 | 33 | 5 | 2 |
subtype2 | 25 | 0 | 0 |
subtype3 | 14 | 3 | 1 |
P value = 0.331 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 27 | 25.3 (15.0) |
subtype1 | 14 | 29.1 (13.0) |
subtype2 | 9 | 21.2 (17.7) |
subtype3 | 4 | 21.2 (16.0) |
P value = 0.182 (Fisher's exact test), Q value = 1
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 52 | 25 | 1 | 2 |
subtype1 | 21 | 16 | 1 | 1 |
subtype2 | 16 | 7 | 0 | 1 |
subtype3 | 15 | 2 | 0 | 0 |
P value = 0.064 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 83 | 2.7 (3.0) |
subtype1 | 41 | 2.2 (2.0) |
subtype2 | 25 | 3.8 (3.6) |
subtype3 | 17 | 2.3 (3.5) |
P value = 0.184 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 5 | 73 |
subtype1 | 0 | 1 | 38 |
subtype2 | 1 | 3 | 20 |
subtype3 | 1 | 1 | 15 |
-
Cluster data file = PAAD-TP.mergedcluster.txt
-
Clinical data file = PAAD-TP.merged_data.txt
-
Number of patients = 93
-
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 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.