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 9 clinical features across 160 patients, 7 significant findings 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.
-
7 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 4 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'HISTOLOGICAL.TYPE'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
-
3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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 |
0.107 (1.00) |
0.524 (1.00) |
0.873 (1.00) |
0.833 (1.00) |
0.611 (1.00) |
0.662 (1.00) |
0.779 (1.00) |
0.861 (1.00) |
AGE | ANOVA |
0.968 (1.00) |
0.0139 (0.889) |
0.00418 (0.272) |
0.141 (1.00) |
0.512 (1.00) |
0.143 (1.00) |
0.366 (1.00) |
0.298 (1.00) |
PATHOLOGY T STAGE | Chi-square test |
0.929 (1.00) |
0.943 (1.00) |
0.769 (1.00) |
0.981 (1.00) |
0.906 (1.00) |
0.618 (1.00) |
0.924 (1.00) |
0.927 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
0.0443 (1.00) |
0.499 (1.00) |
0.361 (1.00) |
0.621 (1.00) |
0.219 (1.00) |
0.405 (1.00) |
0.59 (1.00) |
0.375 (1.00) |
PATHOLOGY M STAGE | Chi-square test |
0.515 (1.00) |
0.414 (1.00) |
0.56 (1.00) |
0.0501 (1.00) |
0.217 (1.00) |
0.0992 (1.00) |
0.142 (1.00) |
0.0517 (1.00) |
HISTOLOGICAL TYPE | Chi-square test |
0.734 (1.00) |
7.05e-15 (5.01e-13) |
7.72e-10 (5.25e-08) |
3.26e-15 (2.35e-13) |
3.65e-06 (0.000241) |
1.16e-12 (7.98e-11) |
4.3e-07 (2.88e-05) |
4.91e-13 (3.44e-11) |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test |
0.731 (1.00) |
0.314 (1.00) |
0.424 (1.00) |
0.674 (1.00) |
0.25 (1.00) |
0.682 (1.00) |
0.0177 (1.00) |
0.214 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.847 (1.00) |
0.387 (1.00) |
0.329 (1.00) |
0.527 (1.00) |
0.441 (1.00) |
0.231 (1.00) |
0.616 (1.00) |
0.849 (1.00) |
NUMBER OF LYMPH NODES | ANOVA |
0.916 (1.00) |
0.612 (1.00) |
0.629 (1.00) |
0.645 (1.00) |
0.684 (1.00) |
0.24 (1.00) |
0.678 (1.00) |
0.585 (1.00) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 46 | 34 | 70 |
P value = 0.107 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 143 | 28 | 0.0 - 177.0 (12.6) |
subtype1 | 44 | 5 | 0.0 - 173.3 (15.0) |
subtype2 | 29 | 8 | 0.1 - 144.2 (15.5) |
subtype3 | 70 | 15 | 0.0 - 177.0 (6.4) |
P value = 0.968 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 149 | 47.4 (13.3) |
subtype1 | 45 | 47.8 (10.3) |
subtype2 | 34 | 47.0 (14.9) |
subtype3 | 70 | 47.3 (14.3) |
P value = 0.929 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 81 | 29 | 3 |
subtype1 | 26 | 9 | 1 |
subtype2 | 14 | 4 | 0 |
subtype3 | 41 | 16 | 2 |
P value = 0.0443 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 73 | 36 |
subtype1 | 20 | 14 |
subtype2 | 9 | 9 |
subtype3 | 44 | 13 |
P value = 0.515 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 61 | 3 | 53 |
subtype1 | 24 | 1 | 14 |
subtype2 | 8 | 0 | 11 |
subtype3 | 29 | 2 | 28 |
P value = 0.734 (Chi-square test), Q value = 1
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 124 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 41 | 1 | 3 | 0 | 1 |
subtype2 | 0 | 30 | 1 | 3 | 0 | 0 |
subtype3 | 2 | 53 | 2 | 10 | 1 | 2 |
P value = 0.731 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 25 | 125 |
subtype1 | 9 | 37 |
subtype2 | 6 | 28 |
subtype3 | 10 | 60 |
P value = 0.847 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 43 | 18.2 (11.7) |
subtype1 | 11 | 17.8 (12.9) |
subtype2 | 9 | 20.2 (7.9) |
subtype3 | 23 | 17.6 (12.7) |
P value = 0.916 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 93 | 1.1 (2.3) |
subtype1 | 29 | 1.2 (1.7) |
subtype2 | 14 | 1.1 (1.4) |
subtype3 | 50 | 1.0 (2.8) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
---|---|---|---|---|---|---|---|
Number of samples | 29 | 21 | 16 | 30 | 25 | 25 | 14 |
P value = 0.524 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 153 | 32 | 0.0 - 177.0 (12.7) |
subtype1 | 29 | 7 | 0.0 - 177.0 (13.9) |
subtype2 | 18 | 4 | 0.6 - 137.2 (21.7) |
subtype3 | 16 | 2 | 0.8 - 134.3 (13.3) |
subtype4 | 27 | 9 | 0.0 - 118.7 (12.4) |
subtype5 | 25 | 5 | 0.1 - 173.3 (5.8) |
subtype6 | 24 | 5 | 0.1 - 97.0 (12.2) |
subtype7 | 14 | 0 | 0.0 - 53.2 (3.3) |
P value = 0.0139 (ANOVA), Q value = 0.89
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 159 | 47.8 (13.4) |
subtype1 | 29 | 47.7 (14.6) |
subtype2 | 21 | 53.0 (10.6) |
subtype3 | 16 | 49.2 (10.6) |
subtype4 | 29 | 42.6 (12.4) |
subtype5 | 25 | 48.4 (14.8) |
subtype6 | 25 | 43.4 (11.7) |
subtype7 | 14 | 56.0 (15.3) |
P value = 0.943 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 87 | 31 | 4 |
subtype1 | 16 | 8 | 1 |
subtype2 | 11 | 5 | 1 |
subtype3 | 7 | 4 | 0 |
subtype4 | 13 | 5 | 1 |
subtype5 | 16 | 3 | 0 |
subtype6 | 15 | 4 | 1 |
subtype7 | 9 | 2 | 0 |
P value = 0.499 (Chi-square test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 79 | 39 |
subtype1 | 15 | 9 |
subtype2 | 10 | 6 |
subtype3 | 7 | 4 |
subtype4 | 14 | 5 |
subtype5 | 10 | 9 |
subtype6 | 14 | 5 |
subtype7 | 9 | 1 |
P value = 0.414 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 68 | 3 | 55 |
subtype1 | 14 | 0 | 11 |
subtype2 | 10 | 1 | 6 |
subtype3 | 6 | 0 | 7 |
subtype4 | 12 | 0 | 8 |
subtype5 | 13 | 0 | 6 |
subtype6 | 7 | 2 | 12 |
subtype7 | 6 | 0 | 5 |
P value = 7.05e-15 (Chi-square test), Q value = 5e-13
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 134 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 29 | 0 | 0 | 0 | 0 |
subtype2 | 1 | 17 | 0 | 2 | 1 | 0 |
subtype3 | 0 | 16 | 0 | 0 | 0 | 0 |
subtype4 | 0 | 30 | 0 | 0 | 0 | 0 |
subtype5 | 0 | 25 | 0 | 0 | 0 | 0 |
subtype6 | 1 | 3 | 4 | 14 | 0 | 3 |
subtype7 | 0 | 14 | 0 | 0 | 0 | 0 |
P value = 0.314 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 30 | 130 |
subtype1 | 8 | 21 |
subtype2 | 6 | 15 |
subtype3 | 1 | 15 |
subtype4 | 7 | 23 |
subtype5 | 4 | 21 |
subtype6 | 2 | 23 |
subtype7 | 2 | 12 |
P value = 0.387 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 45 | 18.4 (11.6) |
subtype1 | 10 | 17.6 (7.3) |
subtype2 | 4 | 18.2 (11.9) |
subtype3 | 6 | 28.8 (16.7) |
subtype4 | 7 | 16.5 (10.0) |
subtype5 | 7 | 17.1 (10.1) |
subtype6 | 6 | 12.9 (13.6) |
subtype7 | 5 | 19.0 (12.4) |
P value = 0.612 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 101 | 1.2 (2.8) |
subtype1 | 17 | 1.4 (2.4) |
subtype2 | 11 | 2.2 (4.8) |
subtype3 | 12 | 1.2 (1.7) |
subtype4 | 15 | 0.8 (1.6) |
subtype5 | 17 | 1.1 (2.0) |
subtype6 | 17 | 1.8 (4.2) |
subtype7 | 12 | 0.1 (0.3) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 55 | 26 | 35 | 30 |
P value = 0.873 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 139 | 24 | 0.0 - 177.0 (12.7) |
subtype1 | 54 | 11 | 0.1 - 177.0 (5.0) |
subtype2 | 24 | 3 | 0.0 - 134.3 (14.7) |
subtype3 | 33 | 5 | 0.1 - 147.4 (14.7) |
subtype4 | 28 | 5 | 0.0 - 118.7 (11.9) |
P value = 0.00418 (ANOVA), Q value = 0.27
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 145 | 47.5 (13.1) |
subtype1 | 55 | 49.6 (14.8) |
subtype2 | 26 | 53.0 (10.7) |
subtype3 | 35 | 44.9 (11.3) |
subtype4 | 29 | 41.8 (11.1) |
P value = 0.769 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 79 | 29 | 3 |
subtype1 | 29 | 13 | 1 |
subtype2 | 14 | 7 | 1 |
subtype3 | 21 | 4 | 1 |
subtype4 | 15 | 5 | 0 |
P value = 0.361 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 71 | 36 |
subtype1 | 24 | 18 |
subtype2 | 13 | 7 |
subtype3 | 19 | 6 |
subtype4 | 15 | 5 |
P value = 0.56 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 62 | 3 | 50 |
subtype1 | 23 | 0 | 21 |
subtype2 | 12 | 1 | 9 |
subtype3 | 14 | 2 | 11 |
subtype4 | 13 | 0 | 9 |
P value = 7.72e-10 (Chi-square test), Q value = 5.2e-08
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 1 | 122 | 4 | 15 | 1 | 3 |
subtype1 | 0 | 55 | 0 | 0 | 0 | 0 |
subtype2 | 1 | 23 | 0 | 2 | 0 | 0 |
subtype3 | 0 | 14 | 4 | 13 | 1 | 3 |
subtype4 | 0 | 30 | 0 | 0 | 0 | 0 |
P value = 0.424 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 28 | 118 |
subtype1 | 10 | 45 |
subtype2 | 7 | 19 |
subtype3 | 4 | 31 |
subtype4 | 7 | 23 |
P value = 0.329 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 18.8 (11.4) |
subtype1 | 19 | 19.4 (11.8) |
subtype2 | 8 | 22.9 (12.7) |
subtype3 | 8 | 12.6 (11.4) |
subtype4 | 7 | 19.9 (7.9) |
P value = 0.629 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 91 | 1.2 (2.8) |
subtype1 | 38 | 1.2 (2.0) |
subtype2 | 16 | 1.8 (4.0) |
subtype3 | 23 | 1.3 (3.7) |
subtype4 | 14 | 0.4 (0.8) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 14 | 97 | 35 |
P value = 0.833 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 139 | 24 | 0.0 - 177.0 (12.7) |
subtype1 | 13 | 2 | 0.0 - 78.7 (11.4) |
subtype2 | 92 | 16 | 0.0 - 177.0 (13.3) |
subtype3 | 34 | 6 | 0.1 - 137.2 (11.2) |
P value = 0.141 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 145 | 47.5 (13.1) |
subtype1 | 14 | 41.6 (8.3) |
subtype2 | 96 | 48.8 (14.0) |
subtype3 | 35 | 46.5 (11.3) |
P value = 0.981 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 79 | 29 | 3 |
subtype1 | 7 | 3 | 0 |
subtype2 | 52 | 19 | 2 |
subtype3 | 20 | 7 | 1 |
P value = 0.621 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 71 | 36 |
subtype1 | 8 | 3 |
subtype2 | 44 | 26 |
subtype3 | 19 | 7 |
P value = 0.0501 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 62 | 3 | 50 |
subtype1 | 7 | 0 | 4 |
subtype2 | 41 | 0 | 34 |
subtype3 | 14 | 3 | 12 |
P value = 3.26e-15 (Chi-square test), Q value = 2.3e-13
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 1 | 122 | 4 | 15 | 1 | 3 |
subtype1 | 0 | 14 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 97 | 0 | 0 | 0 | 0 |
subtype3 | 1 | 11 | 4 | 15 | 1 | 3 |
P value = 0.674 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 28 | 118 |
subtype1 | 2 | 12 |
subtype2 | 21 | 76 |
subtype3 | 5 | 30 |
P value = 0.527 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 42 | 18.8 (11.4) |
subtype1 | 4 | 23.2 (6.4) |
subtype2 | 30 | 19.1 (11.3) |
subtype3 | 8 | 15.4 (13.9) |
P value = 0.645 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 91 | 1.2 (2.8) |
subtype1 | 8 | 0.4 (0.7) |
subtype2 | 61 | 1.2 (2.6) |
subtype3 | 22 | 1.5 (3.7) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 63 | 45 | 50 |
P value = 0.611 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 151 | 31 | 0.0 - 177.0 (12.7) |
subtype1 | 60 | 12 | 0.0 - 177.0 (12.5) |
subtype2 | 42 | 11 | 0.0 - 147.4 (13.3) |
subtype3 | 49 | 8 | 0.1 - 137.2 (12.8) |
P value = 0.512 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 157 | 47.6 (13.4) |
subtype1 | 62 | 46.4 (14.9) |
subtype2 | 45 | 49.4 (14.0) |
subtype3 | 50 | 47.6 (10.7) |
P value = 0.906 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 86 | 31 | 4 |
subtype1 | 30 | 11 | 1 |
subtype2 | 25 | 8 | 2 |
subtype3 | 31 | 12 | 1 |
P value = 0.219 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 78 | 39 |
subtype1 | 24 | 17 |
subtype2 | 22 | 12 |
subtype3 | 32 | 10 |
P value = 0.217 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 68 | 3 | 54 |
subtype1 | 25 | 0 | 18 |
subtype2 | 21 | 0 | 16 |
subtype3 | 22 | 3 | 20 |
P value = 3.65e-06 (Chi-square test), Q value = 0.00024
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 132 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 63 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 41 | 0 | 3 | 0 | 1 |
subtype3 | 2 | 28 | 4 | 13 | 1 | 2 |
P value = 0.25 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 30 | 128 |
subtype1 | 16 | 47 |
subtype2 | 6 | 39 |
subtype3 | 8 | 42 |
P value = 0.441 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 18.2 (11.6) |
subtype1 | 21 | 17.2 (11.3) |
subtype2 | 14 | 21.4 (11.1) |
subtype3 | 9 | 15.5 (13.2) |
P value = 0.684 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 100 | 1.2 (2.8) |
subtype1 | 33 | 1.2 (2.9) |
subtype2 | 34 | 1.6 (2.7) |
subtype3 | 33 | 1.0 (2.8) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 63 | 50 | 45 |
P value = 0.662 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 151 | 31 | 0.0 - 177.0 (12.7) |
subtype1 | 62 | 16 | 0.0 - 177.0 (15.0) |
subtype2 | 46 | 7 | 0.0 - 173.3 (12.0) |
subtype3 | 43 | 8 | 0.1 - 137.2 (9.7) |
P value = 0.143 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 157 | 47.6 (13.4) |
subtype1 | 63 | 50.2 (14.2) |
subtype2 | 49 | 46.4 (14.2) |
subtype3 | 45 | 45.4 (10.7) |
P value = 0.618 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 86 | 31 | 4 |
subtype1 | 35 | 14 | 2 |
subtype2 | 24 | 10 | 0 |
subtype3 | 27 | 7 | 2 |
P value = 0.405 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 78 | 39 |
subtype1 | 30 | 20 |
subtype2 | 23 | 10 |
subtype3 | 25 | 9 |
P value = 0.0992 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 68 | 3 | 54 |
subtype1 | 32 | 0 | 22 |
subtype2 | 18 | 0 | 16 |
subtype3 | 18 | 3 | 16 |
P value = 1.16e-12 (Chi-square test), Q value = 8e-11
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 132 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 63 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 50 | 0 | 0 | 0 | 0 |
subtype3 | 2 | 19 | 4 | 16 | 1 | 3 |
P value = 0.682 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 30 | 128 |
subtype1 | 14 | 49 |
subtype2 | 8 | 42 |
subtype3 | 8 | 37 |
P value = 0.231 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 18.2 (11.6) |
subtype1 | 21 | 21.2 (12.1) |
subtype2 | 13 | 16.4 (9.1) |
subtype3 | 10 | 14.2 (12.6) |
P value = 0.24 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 100 | 1.2 (2.8) |
subtype1 | 45 | 1.7 (3.1) |
subtype2 | 27 | 0.5 (0.8) |
subtype3 | 28 | 1.2 (3.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 63 | 45 | 50 |
P value = 0.779 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 151 | 31 | 0.0 - 177.0 (12.7) |
subtype1 | 60 | 14 | 0.0 - 177.0 (15.6) |
subtype2 | 43 | 10 | 0.0 - 147.4 (8.8) |
subtype3 | 48 | 7 | 0.1 - 137.2 (11.2) |
P value = 0.366 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 157 | 47.6 (13.4) |
subtype1 | 62 | 46.3 (15.2) |
subtype2 | 45 | 50.0 (13.9) |
subtype3 | 50 | 47.2 (10.1) |
P value = 0.924 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 86 | 31 | 4 |
subtype1 | 31 | 10 | 1 |
subtype2 | 25 | 10 | 2 |
subtype3 | 30 | 11 | 1 |
P value = 0.59 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 78 | 39 |
subtype1 | 26 | 16 |
subtype2 | 23 | 12 |
subtype3 | 29 | 11 |
P value = 0.142 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 68 | 3 | 54 |
subtype1 | 25 | 0 | 18 |
subtype2 | 23 | 0 | 15 |
subtype3 | 20 | 3 | 21 |
P value = 4.3e-07 (Chi-square test), Q value = 2.9e-05
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 132 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 63 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 42 | 0 | 2 | 0 | 1 |
subtype3 | 2 | 27 | 4 | 14 | 1 | 2 |
P value = 0.0177 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 30 | 128 |
subtype1 | 19 | 44 |
subtype2 | 5 | 40 |
subtype3 | 6 | 44 |
P value = 0.616 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 18.2 (11.6) |
subtype1 | 20 | 17.7 (10.7) |
subtype2 | 13 | 20.7 (11.2) |
subtype3 | 11 | 16.1 (13.9) |
P value = 0.678 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 100 | 1.2 (2.8) |
subtype1 | 35 | 1.3 (3.0) |
subtype2 | 35 | 1.5 (2.7) |
subtype3 | 30 | 0.9 (2.7) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 60 | 57 | 41 |
P value = 0.861 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 151 | 31 | 0.0 - 177.0 (12.7) |
subtype1 | 57 | 15 | 0.0 - 177.0 (14.9) |
subtype2 | 55 | 10 | 0.0 - 173.3 (12.6) |
subtype3 | 39 | 6 | 0.0 - 137.2 (7.9) |
P value = 0.298 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 157 | 47.6 (13.4) |
subtype1 | 60 | 49.7 (15.2) |
subtype2 | 56 | 46.7 (13.0) |
subtype3 | 41 | 45.9 (10.7) |
P value = 0.927 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 86 | 31 | 4 |
subtype1 | 33 | 10 | 2 |
subtype2 | 30 | 13 | 1 |
subtype3 | 23 | 8 | 1 |
P value = 0.375 (Fisher's exact test), Q value = 1
nPatients | 0 | 1 |
---|---|---|
ALL | 78 | 39 |
subtype1 | 27 | 17 |
subtype2 | 28 | 15 |
subtype3 | 23 | 7 |
P value = 0.0517 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 68 | 3 | 54 |
subtype1 | 29 | 0 | 19 |
subtype2 | 24 | 0 | 20 |
subtype3 | 15 | 3 | 15 |
P value = 4.91e-13 (Chi-square test), Q value = 3.4e-11
nPatients | ADENOSQUAMOUS | CERVICAL SQUAMOUS CELL CARCINOMA | ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | ENDOCERVICAL TYPE OF ADENOCARCINOMA | ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE |
---|---|---|---|---|---|---|
ALL | 2 | 132 | 4 | 16 | 1 | 3 |
subtype1 | 0 | 60 | 0 | 0 | 0 | 0 |
subtype2 | 0 | 56 | 0 | 1 | 0 | 0 |
subtype3 | 2 | 16 | 4 | 15 | 1 | 3 |
P value = 0.214 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 30 | 128 |
subtype1 | 13 | 47 |
subtype2 | 13 | 44 |
subtype3 | 4 | 37 |
P value = 0.849 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 44 | 18.2 (11.6) |
subtype1 | 19 | 18.8 (10.8) |
subtype2 | 16 | 18.6 (12.0) |
subtype3 | 9 | 16.2 (13.6) |
P value = 0.585 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 100 | 1.2 (2.8) |
subtype1 | 40 | 1.2 (2.1) |
subtype2 | 36 | 1.6 (3.6) |
subtype3 | 24 | 0.8 (2.3) |
-
Cluster data file = CESC-TP.mergedcluster.txt
-
Clinical data file = CESC-TP.merged_data.txt
-
Number of patients = 160
-
Number of clustering approaches = 8
-
Number of selected clinical features = 9
-
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.