This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 10 different clustering approaches and 10 clinical features across 36 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes do not correlate to any clinical features.
-
CNMF clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on RPPA data identified 4 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 6 subtypes that do not correlate to any clinical features.
-
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.
-
2 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
-
7 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
RACE |
Statistical Tests | logrank test | Kruskal-Wallis (anova) | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Copy Number Ratio CNMF subtypes |
0.496 (0.976) |
0.837 (1.00) |
0.644 (0.976) |
1 (1.00) |
0.344 (0.976) |
1 (1.00) |
0.749 (0.993) |
0.35 (0.976) |
0.598 (0.976) |
0.236 (0.976) |
METHLYATION CNMF |
0.884 (1.00) |
0.221 (0.976) |
0.22 (0.976) |
0.755 (0.993) |
0.591 (0.976) |
0.588 (0.976) |
0.637 (0.976) |
0.124 (0.976) |
0.142 (0.976) |
0.701 (0.976) |
RPPA CNMF subtypes |
0.187 (0.976) |
0.0209 (0.926) |
0.916 (1.00) |
0.776 (0.998) |
0.516 (0.976) |
0.344 (0.976) |
0.809 (1.00) |
0.515 (0.976) |
0.517 (0.976) |
0.328 (0.976) |
RPPA cHierClus subtypes |
0.473 (0.976) |
0.0524 (0.926) |
0.469 (0.976) |
0.398 (0.976) |
0.286 (0.976) |
0.149 (0.976) |
0.689 (0.976) |
0.511 (0.976) |
0.594 (0.976) |
0.603 (0.976) |
RNAseq CNMF subtypes |
0.905 (1.00) |
0.481 (0.976) |
0.651 (0.976) |
0.611 (0.976) |
0.568 (0.976) |
1 (1.00) |
0.0555 (0.926) |
0.369 (0.976) |
0.0997 (0.976) |
0.482 (0.976) |
RNAseq cHierClus subtypes |
0.167 (0.976) |
0.372 (0.976) |
0.412 (0.976) |
0.722 (0.976) |
0.0143 (0.926) |
0.24 (0.976) |
0.145 (0.976) |
0.56 (0.976) |
0.409 (0.976) |
0.358 (0.976) |
MIRSEQ CNMF |
0.637 (0.976) |
0.421 (0.976) |
0.501 (0.976) |
0.677 (0.976) |
0.592 (0.976) |
0.228 (0.976) |
0.935 (1.00) |
0.039 (0.926) |
0.686 (0.976) |
0.707 (0.976) |
MIRSEQ CHIERARCHICAL |
0.987 (1.00) |
0.988 (1.00) |
0.703 (0.976) |
0.905 (1.00) |
1 (1.00) |
0.871 (1.00) |
0.0511 (0.926) |
0.502 (0.976) |
0.213 (0.976) |
0.465 (0.976) |
MIRseq Mature CNMF subtypes |
0.478 (0.976) |
0.619 (0.976) |
0.979 (1.00) |
0.586 (0.976) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.812 (1.00) |
0.283 (0.976) |
0.778 (0.998) |
MIRseq Mature cHierClus subtypes |
0.654 (0.976) |
0.171 (0.976) |
0.967 (1.00) |
0.909 (1.00) |
0.984 (1.00) |
0.564 (0.976) |
0.56 (0.976) |
0.088 (0.976) |
0.268 (0.976) |
0.714 (0.976) |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 19 | 17 |
P value = 0.496 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 19 | 7 | 0.3 - 65.0 (13.2) |
subtype2 | 17 | 11 | 0.7 - 63.8 (20.6) |
P value = 0.837 (Wilcoxon-test), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 19 | 63.2 (12.3) |
subtype2 | 17 | 62.9 (13.8) |
P value = 0.644 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 10 | 3 | 1 | 1 | 2 | 2 |
subtype2 | 9 | 6 | 0 | 1 | 0 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 10 | 6 | 3 |
subtype2 | 9 | 6 | 2 |
P value = 0.344 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 13 | 4 |
subtype2 | 13 | 1 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 15 | 3 |
subtype2 | 13 | 2 |
P value = 0.749 (Fisher's exact test), Q value = 0.99
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 10 | 9 |
subtype2 | 10 | 7 |
P value = 0.35 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 2 | 3 | 14 |
subtype2 | 0 | 1 | 16 |
P value = 0.598 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 16 | 2 | 1 |
subtype2 | 12 | 3 | 2 |
P value = 0.236 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 3 | 1 | 15 |
subtype2 | 0 | 1 | 16 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 13 | 10 | 13 |
P value = 0.884 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 13 | 4 | 0.3 - 48.8 (13.2) |
subtype2 | 10 | 7 | 0.8 - 65.0 (19.6) |
subtype3 | 13 | 7 | 1.6 - 63.8 (20.6) |
P value = 0.221 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 13 | 65.8 (10.1) |
subtype2 | 10 | 58.8 (11.2) |
subtype3 | 13 | 63.5 (16.2) |
P value = 0.22 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 8 | 2 | 1 | 0 | 0 | 2 |
subtype2 | 6 | 2 | 0 | 2 | 0 | 0 |
subtype3 | 5 | 5 | 0 | 0 | 2 | 1 |
P value = 0.755 (Fisher's exact test), Q value = 0.99
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 8 | 3 | 2 |
subtype2 | 6 | 3 | 1 |
subtype3 | 5 | 6 | 2 |
P value = 0.591 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 9 | 2 |
subtype2 | 7 | 0 |
subtype3 | 10 | 3 |
P value = 0.588 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 9 | 2 |
subtype2 | 7 | 2 |
subtype3 | 12 | 1 |
P value = 0.637 (Fisher's exact test), Q value = 0.98
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 6 | 7 |
subtype2 | 7 | 3 |
subtype3 | 7 | 6 |
P value = 0.124 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 2 | 2 | 9 |
subtype2 | 0 | 2 | 8 |
subtype3 | 0 | 0 | 13 |
P value = 0.142 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 11 | 0 | 2 |
subtype2 | 8 | 1 | 1 |
subtype3 | 9 | 4 | 0 |
P value = 0.701 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 1 | 10 |
subtype2 | 0 | 1 | 9 |
subtype3 | 1 | 0 | 12 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 10 | 8 | 12 |
P value = 0.187 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 15 | 0.3 - 65.0 (18.1) |
subtype1 | 10 | 7 | 0.3 - 63.8 (11.9) |
subtype2 | 8 | 3 | 5.6 - 65.0 (18.8) |
subtype3 | 12 | 5 | 0.8 - 46.1 (22.0) |
P value = 0.0209 (Kruskal-Wallis (anova)), Q value = 0.93
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 63.1 (13.8) |
subtype1 | 10 | 71.1 (2.8) |
subtype2 | 8 | 65.2 (14.5) |
subtype3 | 12 | 55.1 (15.1) |
P value = 0.916 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 17 | 6 | 1 | 2 | 2 | 2 |
subtype1 | 5 | 2 | 1 | 0 | 1 | 1 |
subtype2 | 6 | 2 | 0 | 0 | 0 | 0 |
subtype3 | 6 | 2 | 0 | 2 | 1 | 1 |
P value = 0.776 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 17 | 9 | 4 |
subtype1 | 5 | 3 | 2 |
subtype2 | 6 | 2 | 0 |
subtype3 | 6 | 4 | 2 |
P value = 0.516 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 4 |
subtype1 | 7 | 2 |
subtype2 | 7 | 0 |
subtype3 | 8 | 2 |
P value = 0.344 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 24 | 4 |
subtype1 | 8 | 1 |
subtype2 | 8 | 0 |
subtype3 | 8 | 3 |
P value = 0.809 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 13 |
subtype1 | 6 | 4 |
subtype2 | 5 | 3 |
subtype3 | 6 | 6 |
P value = 0.515 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 1 | 4 | 25 |
subtype1 | 1 | 2 | 7 |
subtype2 | 0 | 0 | 8 |
subtype3 | 0 | 2 | 10 |
P value = 0.517 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 24 | 3 | 3 |
subtype1 | 7 | 1 | 2 |
subtype2 | 7 | 0 | 1 |
subtype3 | 10 | 2 | 0 |
P value = 0.328 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 2 | 26 |
subtype1 | 2 | 0 | 8 |
subtype2 | 0 | 1 | 7 |
subtype3 | 0 | 1 | 11 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 6 | 7 | 8 | 9 |
P value = 0.473 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 30 | 15 | 0.3 - 65.0 (18.1) |
subtype1 | 6 | 5 | 8.9 - 63.8 (15.5) |
subtype2 | 7 | 2 | 5.6 - 65.0 (17.1) |
subtype3 | 8 | 4 | 0.7 - 35.5 (21.8) |
subtype4 | 9 | 4 | 0.3 - 46.1 (18.1) |
P value = 0.0524 (Kruskal-Wallis (anova)), Q value = 0.93
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 30 | 63.1 (13.8) |
subtype1 | 6 | 70.7 (3.7) |
subtype2 | 7 | 63.4 (14.6) |
subtype3 | 8 | 69.0 (9.4) |
subtype4 | 9 | 52.7 (15.5) |
P value = 0.469 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 17 | 6 | 1 | 2 | 2 | 2 |
subtype1 | 3 | 0 | 1 | 0 | 1 | 1 |
subtype2 | 5 | 2 | 0 | 0 | 0 | 0 |
subtype3 | 6 | 2 | 0 | 0 | 0 | 0 |
subtype4 | 3 | 2 | 0 | 2 | 1 | 1 |
P value = 0.398 (Fisher's exact test), Q value = 0.98
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 17 | 9 | 4 |
subtype1 | 3 | 1 | 2 |
subtype2 | 5 | 2 | 0 |
subtype3 | 6 | 2 | 0 |
subtype4 | 3 | 4 | 2 |
P value = 0.286 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 22 | 4 |
subtype1 | 4 | 2 |
subtype2 | 6 | 0 |
subtype3 | 6 | 0 |
subtype4 | 6 | 2 |
P value = 0.149 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 24 | 4 |
subtype1 | 5 | 1 |
subtype2 | 7 | 0 |
subtype3 | 7 | 0 |
subtype4 | 5 | 3 |
P value = 0.689 (Fisher's exact test), Q value = 0.98
nPatients | FEMALE | MALE |
---|---|---|
ALL | 17 | 13 |
subtype1 | 3 | 3 |
subtype2 | 4 | 3 |
subtype3 | 6 | 2 |
subtype4 | 4 | 5 |
P value = 0.511 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 1 | 4 | 25 |
subtype1 | 1 | 1 | 4 |
subtype2 | 0 | 0 | 7 |
subtype3 | 0 | 1 | 7 |
subtype4 | 0 | 2 | 7 |
P value = 0.594 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 24 | 3 | 3 |
subtype1 | 4 | 1 | 1 |
subtype2 | 6 | 0 | 1 |
subtype3 | 7 | 0 | 1 |
subtype4 | 7 | 2 | 0 |
P value = 0.603 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 2 | 2 | 26 |
subtype1 | 1 | 0 | 5 |
subtype2 | 0 | 1 | 6 |
subtype3 | 1 | 1 | 6 |
subtype4 | 0 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 12 | 15 | 9 |
P value = 0.905 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 12 | 5 | 3.2 - 48.8 (16.3) |
subtype2 | 15 | 8 | 1.6 - 63.8 (20.0) |
subtype3 | 9 | 5 | 0.3 - 65.0 (13.4) |
P value = 0.481 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 12 | 66.3 (11.7) |
subtype2 | 15 | 59.2 (15.1) |
subtype3 | 9 | 65.0 (9.4) |
P value = 0.651 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 7 | 2 | 1 | 0 | 0 | 2 |
subtype2 | 6 | 5 | 0 | 1 | 2 | 1 |
subtype3 | 6 | 2 | 0 | 1 | 0 | 0 |
P value = 0.611 (Fisher's exact test), Q value = 0.98
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 7 | 3 | 2 |
subtype2 | 6 | 6 | 3 |
subtype3 | 6 | 3 | 0 |
P value = 0.568 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 8 | 2 |
subtype2 | 11 | 3 |
subtype3 | 7 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 8 | 2 |
subtype2 | 13 | 2 |
subtype3 | 7 | 1 |
P value = 0.0555 (Fisher's exact test), Q value = 0.93
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 7 | 5 |
subtype2 | 11 | 4 |
subtype3 | 2 | 7 |
P value = 0.369 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 2 | 2 | 8 |
subtype2 | 0 | 1 | 14 |
subtype3 | 0 | 1 | 8 |
P value = 0.0997 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 11 | 0 | 1 |
subtype2 | 12 | 3 | 0 |
subtype3 | 5 | 2 | 2 |
P value = 0.482 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 10 |
subtype2 | 1 | 2 | 12 |
subtype3 | 0 | 0 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 4 | 5 | 5 | 9 | 6 | 5 | 2 |
P value = 0.167 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 34 | 17 | 0.3 - 65.0 (18.1) |
subtype1 | 4 | 3 | 3.2 - 13.2 (10.0) |
subtype2 | 5 | 1 | 10.2 - 48.8 (18.1) |
subtype3 | 5 | 1 | 6.8 - 35.5 (20.6) |
subtype4 | 9 | 5 | 0.3 - 65.0 (13.4) |
subtype5 | 6 | 5 | 5.6 - 63.8 (35.9) |
subtype6 | 5 | 2 | 1.6 - 33.4 (12.7) |
P value = 0.372 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 34 | 64.6 (11.3) |
subtype1 | 4 | 65.2 (9.1) |
subtype2 | 5 | 60.6 (13.1) |
subtype3 | 5 | 73.0 (7.6) |
subtype4 | 9 | 65.0 (9.4) |
subtype5 | 6 | 61.3 (8.0) |
subtype6 | 5 | 63.0 (19.2) |
P value = 0.412 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 18 | 9 | 1 | 2 | 1 | 3 |
subtype1 | 2 | 0 | 0 | 0 | 0 | 2 |
subtype2 | 2 | 2 | 1 | 0 | 0 | 0 |
subtype3 | 4 | 1 | 0 | 0 | 0 | 0 |
subtype4 | 6 | 2 | 0 | 1 | 0 | 0 |
subtype5 | 3 | 2 | 0 | 1 | 0 | 0 |
subtype6 | 1 | 2 | 0 | 0 | 1 | 1 |
P value = 0.722 (Fisher's exact test), Q value = 0.98
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 18 | 11 | 5 |
subtype1 | 2 | 1 | 1 |
subtype2 | 2 | 2 | 1 |
subtype3 | 4 | 1 | 0 |
subtype4 | 6 | 3 | 0 |
subtype5 | 3 | 2 | 1 |
subtype6 | 1 | 2 | 2 |
P value = 0.0143 (Fisher's exact test), Q value = 0.93
nPatients | 0 | 1 |
---|---|---|
ALL | 25 | 4 |
subtype1 | 1 | 2 |
subtype2 | 4 | 0 |
subtype3 | 5 | 0 |
subtype4 | 7 | 0 |
subtype5 | 5 | 0 |
subtype6 | 3 | 2 |
P value = 0.24 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 1 | 2 |
subtype2 | 4 | 0 |
subtype3 | 5 | 0 |
subtype4 | 7 | 1 |
subtype5 | 5 | 1 |
subtype6 | 4 | 1 |
P value = 0.145 (Fisher's exact test), Q value = 0.98
nPatients | FEMALE | MALE |
---|---|---|
ALL | 18 | 16 |
subtype1 | 1 | 3 |
subtype2 | 4 | 1 |
subtype3 | 3 | 2 |
subtype4 | 2 | 7 |
subtype5 | 5 | 1 |
subtype6 | 3 | 2 |
P value = 0.56 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 28 |
subtype1 | 1 | 1 | 2 |
subtype2 | 1 | 0 | 4 |
subtype3 | 0 | 1 | 4 |
subtype4 | 0 | 1 | 8 |
subtype5 | 0 | 1 | 5 |
subtype6 | 0 | 0 | 5 |
P value = 0.409 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 26 | 5 | 3 |
subtype1 | 3 | 0 | 1 |
subtype2 | 5 | 0 | 0 |
subtype3 | 4 | 1 | 0 |
subtype4 | 5 | 2 | 2 |
subtype5 | 6 | 0 | 0 |
subtype6 | 3 | 2 | 0 |
P value = 0.358 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 1 | 30 |
subtype1 | 1 | 0 | 3 |
subtype2 | 1 | 0 | 4 |
subtype3 | 0 | 0 | 5 |
subtype4 | 0 | 0 | 9 |
subtype5 | 1 | 1 | 4 |
subtype6 | 0 | 0 | 5 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 9 | 6 | 10 | 11 |
P value = 0.637 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 9 | 2 | 0.7 - 48.8 (18.1) |
subtype2 | 6 | 5 | 0.8 - 65.0 (17.8) |
subtype3 | 10 | 5 | 1.6 - 40.1 (18.8) |
subtype4 | 11 | 6 | 0.3 - 63.8 (18.2) |
P value = 0.421 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 9 | 67.6 (10.7) |
subtype2 | 6 | 58.8 (11.8) |
subtype3 | 10 | 65.3 (10.3) |
subtype4 | 11 | 59.5 (16.5) |
P value = 0.501 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 5 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 2 | 2 | 0 | 2 | 0 | 0 |
subtype3 | 5 | 2 | 0 | 0 | 1 | 2 |
subtype4 | 7 | 3 | 0 | 0 | 1 | 0 |
P value = 0.677 (Fisher's exact test), Q value = 0.98
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 5 | 2 | 2 |
subtype2 | 2 | 3 | 1 |
subtype3 | 5 | 3 | 2 |
subtype4 | 7 | 4 | 0 |
P value = 0.592 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 7 | 1 |
subtype2 | 4 | 0 |
subtype3 | 7 | 3 |
subtype4 | 8 | 1 |
P value = 0.228 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 6 | 1 |
subtype2 | 4 | 2 |
subtype3 | 8 | 2 |
subtype4 | 10 | 0 |
P value = 0.935 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 4 |
subtype2 | 3 | 3 |
subtype3 | 5 | 5 |
subtype4 | 7 | 4 |
P value = 0.039 (Fisher's exact test), Q value = 0.93
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 2 | 0 | 7 |
subtype2 | 0 | 2 | 4 |
subtype3 | 0 | 2 | 8 |
subtype4 | 0 | 0 | 11 |
P value = 0.686 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 8 | 0 | 1 |
subtype2 | 4 | 1 | 1 |
subtype3 | 7 | 2 | 1 |
subtype4 | 9 | 2 | 0 |
P value = 0.707 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 7 |
subtype2 | 0 | 0 | 6 |
subtype3 | 0 | 1 | 9 |
subtype4 | 1 | 1 | 9 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 8 | 10 | 4 | 5 | 5 | 4 |
P value = 0.987 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 8 | 3 | 3.2 - 48.8 (13.9) |
subtype2 | 10 | 4 | 1.6 - 40.1 (22.0) |
subtype3 | 4 | 3 | 5.6 - 63.8 (25.2) |
subtype4 | 5 | 4 | 0.7 - 65.0 (21.0) |
subtype5 | 5 | 3 | 5.1 - 31.7 (18.2) |
subtype6 | 4 | 1 | 0.3 - 35.2 (7.1) |
P value = 0.988 (Kruskal-Wallis (anova)), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 8 | 62.1 (11.7) |
subtype2 | 10 | 66.1 (11.3) |
subtype3 | 4 | 60.2 (19.7) |
subtype4 | 5 | 64.4 (11.8) |
subtype5 | 5 | 58.4 (18.7) |
subtype6 | 4 | 64.0 (9.8) |
P value = 0.703 (Fisher's exact test), Q value = 0.98
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 4 | 2 | 1 | 0 | 0 | 1 |
subtype2 | 6 | 2 | 0 | 0 | 0 | 2 |
subtype3 | 1 | 2 | 0 | 0 | 1 | 0 |
subtype4 | 2 | 2 | 0 | 1 | 0 | 0 |
subtype5 | 3 | 1 | 0 | 0 | 1 | 0 |
subtype6 | 3 | 0 | 0 | 1 | 0 | 0 |
P value = 0.905 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 4 | 2 | 2 |
subtype2 | 6 | 3 | 1 |
subtype3 | 1 | 3 | 0 |
subtype4 | 2 | 2 | 1 |
subtype5 | 3 | 1 | 1 |
subtype6 | 3 | 1 | 0 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 5 | 1 |
subtype2 | 8 | 2 |
subtype3 | 3 | 1 |
subtype4 | 4 | 0 |
subtype5 | 3 | 1 |
subtype6 | 3 | 0 |
P value = 0.871 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 5 | 1 |
subtype2 | 8 | 2 |
subtype3 | 4 | 0 |
subtype4 | 3 | 1 |
subtype5 | 5 | 0 |
subtype6 | 3 | 1 |
P value = 0.0511 (Fisher's exact test), Q value = 0.93
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 3 |
subtype2 | 4 | 6 |
subtype3 | 3 | 1 |
subtype4 | 3 | 2 |
subtype5 | 5 | 0 |
subtype6 | 0 | 4 |
P value = 0.502 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 2 | 0 | 6 |
subtype2 | 0 | 2 | 8 |
subtype3 | 0 | 0 | 4 |
subtype4 | 0 | 1 | 4 |
subtype5 | 0 | 0 | 5 |
subtype6 | 0 | 1 | 3 |
P value = 0.213 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 8 | 0 | 0 |
subtype2 | 8 | 1 | 1 |
subtype3 | 3 | 1 | 0 |
subtype4 | 3 | 0 | 2 |
subtype5 | 3 | 2 | 0 |
subtype6 | 3 | 1 | 0 |
P value = 0.465 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 0 | 6 |
subtype2 | 0 | 1 | 9 |
subtype3 | 1 | 0 | 3 |
subtype4 | 0 | 0 | 5 |
subtype5 | 0 | 1 | 4 |
subtype6 | 0 | 0 | 4 |
Cluster Labels | 1 | 2 |
---|---|---|
Number of samples | 15 | 21 |
P value = 0.478 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 15 | 8 | 0.3 - 63.8 (13.4) |
subtype2 | 21 | 10 | 0.7 - 65.0 (20.6) |
P value = 0.619 (Wilcoxon-test), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 15 | 60.6 (14.7) |
subtype2 | 21 | 64.8 (11.4) |
P value = 0.979 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 9 | 3 | 0 | 1 | 1 | 1 |
subtype2 | 10 | 6 | 1 | 1 | 1 | 2 |
P value = 0.586 (Fisher's exact test), Q value = 0.98
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 9 | 5 | 1 |
subtype2 | 10 | 7 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 10 | 2 |
subtype2 | 16 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 12 | 2 |
subtype2 | 16 | 3 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 8 | 7 |
subtype2 | 12 | 9 |
P value = 0.812 (Fisher's exact test), Q value = 1
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 1 | 1 | 13 |
subtype2 | 1 | 3 | 17 |
P value = 0.283 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 12 | 3 | 0 |
subtype2 | 16 | 2 | 3 |
P value = 0.778 (Fisher's exact test), Q value = 1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 2 | 1 | 12 |
subtype2 | 1 | 1 | 19 |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 6 | 3 | 3 | 9 | 5 | 5 | 5 |
P value = 0.654 (logrank test), Q value = 0.98
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 36 | 18 | 0.3 - 65.0 (18.1) |
subtype1 | 6 | 2 | 5.1 - 18.1 (13.9) |
subtype2 | 3 | 2 | 8.9 - 24.4 (23.3) |
subtype3 | 3 | 0 | 10.2 - 48.8 (20.9) |
subtype4 | 9 | 6 | 0.3 - 63.8 (13.4) |
subtype5 | 5 | 2 | 1.6 - 35.5 (12.7) |
subtype6 | 5 | 3 | 0.7 - 65.0 (21.0) |
subtype7 | 5 | 3 | 23.1 - 46.1 (33.4) |
P value = 0.171 (Kruskal-Wallis (anova)), Q value = 0.98
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 36 | 63.0 (12.8) |
subtype1 | 6 | 51.3 (16.8) |
subtype2 | 3 | 65.7 (7.1) |
subtype3 | 3 | 69.0 (8.5) |
subtype4 | 9 | 62.7 (14.8) |
subtype5 | 5 | 72.8 (7.9) |
subtype6 | 5 | 66.2 (9.8) |
subtype7 | 5 | 59.6 (7.1) |
P value = 0.967 (Fisher's exact test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|
ALL | 19 | 9 | 1 | 2 | 2 | 3 |
subtype1 | 3 | 2 | 0 | 0 | 0 | 1 |
subtype2 | 2 | 0 | 0 | 0 | 0 | 1 |
subtype3 | 1 | 1 | 1 | 0 | 0 | 0 |
subtype4 | 5 | 2 | 0 | 1 | 1 | 0 |
subtype5 | 3 | 1 | 0 | 0 | 1 | 0 |
subtype6 | 3 | 2 | 0 | 0 | 0 | 0 |
subtype7 | 2 | 1 | 0 | 1 | 0 | 1 |
P value = 0.909 (Fisher's exact test), Q value = 1
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 19 | 12 | 5 |
subtype1 | 3 | 2 | 1 |
subtype2 | 2 | 1 | 0 |
subtype3 | 1 | 1 | 1 |
subtype4 | 5 | 4 | 0 |
subtype5 | 3 | 1 | 1 |
subtype6 | 3 | 2 | 0 |
subtype7 | 2 | 1 | 2 |
P value = 0.984 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 26 | 5 |
subtype1 | 4 | 1 |
subtype2 | 2 | 1 |
subtype3 | 3 | 0 |
subtype4 | 6 | 1 |
subtype5 | 4 | 1 |
subtype6 | 4 | 0 |
subtype7 | 3 | 1 |
P value = 0.564 (Fisher's exact test), Q value = 0.98
nPatients | 0 | 1 |
---|---|---|
ALL | 28 | 5 |
subtype1 | 4 | 1 |
subtype2 | 2 | 1 |
subtype3 | 3 | 0 |
subtype4 | 7 | 1 |
subtype5 | 5 | 0 |
subtype6 | 4 | 0 |
subtype7 | 3 | 2 |
P value = 0.56 (Fisher's exact test), Q value = 0.98
nPatients | FEMALE | MALE |
---|---|---|
ALL | 20 | 16 |
subtype1 | 5 | 1 |
subtype2 | 1 | 2 |
subtype3 | 2 | 1 |
subtype4 | 4 | 5 |
subtype5 | 2 | 3 |
subtype6 | 2 | 3 |
subtype7 | 4 | 1 |
P value = 0.088 (Fisher's exact test), Q value = 0.98
nPatients | CHOLANGIOCARCINOMA; DISTAL | CHOLANGIOCARCINOMA; HILAR/PERIHILAR | CHOLANGIOCARCINOMA; INTRAHEPATIC |
---|---|---|---|
ALL | 2 | 4 | 30 |
subtype1 | 1 | 0 | 5 |
subtype2 | 0 | 2 | 1 |
subtype3 | 1 | 0 | 2 |
subtype4 | 0 | 1 | 8 |
subtype5 | 0 | 0 | 5 |
subtype6 | 0 | 0 | 5 |
subtype7 | 0 | 1 | 4 |
P value = 0.268 (Fisher's exact test), Q value = 0.98
nPatients | R0 | R1 | RX |
---|---|---|---|
ALL | 28 | 5 | 3 |
subtype1 | 5 | 1 | 0 |
subtype2 | 1 | 1 | 1 |
subtype3 | 3 | 0 | 0 |
subtype4 | 7 | 2 | 0 |
subtype5 | 4 | 1 | 0 |
subtype6 | 3 | 0 | 2 |
subtype7 | 5 | 0 | 0 |
P value = 0.714 (Fisher's exact test), Q value = 0.98
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 3 | 2 | 31 |
subtype1 | 1 | 1 | 4 |
subtype2 | 0 | 0 | 3 |
subtype3 | 1 | 0 | 2 |
subtype4 | 1 | 0 | 8 |
subtype5 | 0 | 0 | 5 |
subtype6 | 0 | 0 | 5 |
subtype7 | 0 | 1 | 4 |
-
Cluster data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/20125181/CHOL-TP.mergedcluster.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/19775070/CHOL-TP.merged_data.txt
-
Number of patients = 36
-
Number of clustering approaches = 10
-
Number of selected clinical features = 10
-
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.