This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.
Testing the association between 2 variables and 39 clinical features across 38 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one variables.
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1 variable correlated to 'AGE_mutation.rate'.
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MUTATIONRATE_NONSYNONYMOUS
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2 variables correlated to 'LOCATION_OF_POSITIVE_MARGINS'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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No variables correlated to 'Time to Death', 'AGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'NUMBER.OF.LYMPH.NODES', 'RACE', 'WEIGHT_KG_AT_DIAGNOSIS', 'TUMOR_STATUS', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_TYPE', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'LYMPH_NODE_LOCATION', 'MENOPAUSE_STATUS', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'KERATINIZATION_SQUAMOUS_CELL', 'INITIAL_PATHOLOGIC_DX_YEAR', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CERVIX_SUV_RESULTS', 'AJCC_TUMOR_PATHOLOGIC_PT', and 'AGE_AT_DIAGNOSIS'.
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of variables that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant variables | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
AGE | Linear Regression Analysis | N=1 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
PATHOLOGY M STAGE | Wilcoxon test | N=0 | ||||
HISTOLOGICAL TYPE | Wilcoxon test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
RACE | Kruskal-Wallis test | N=0 | ||||
WEIGHT_KG_AT_DIAGNOSIS | Spearman correlation test | N=0 | ||||
TUMOR_STATUS | Wilcoxon test | N=0 | ||||
NEOPLASMHISTOLOGICGRADE | Kruskal-Wallis test | N=0 | ||||
TOBACCO_SMOKING_YEAR_STOPPED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_HISTORY | Kruskal-Wallis test | N=0 | ||||
PATIENT AGEBEGANSMOKINGINYEARS | Spearman correlation test | N=0 | ||||
RADIATION_THERAPY_TYPE | Kruskal-Wallis test | N=0 | ||||
PREGNANCIES_COUNT_TOTAL | Spearman correlation test | N=0 | ||||
PREGNANCIES_COUNT_STILLBIRTH | Spearman correlation test | N=0 | ||||
PATIENT PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Spearman correlation test | N=0 | ||||
PREGNANCIES_COUNT_LIVE_BIRTH | Spearman correlation test | N=0 | ||||
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Spearman correlation test | N=0 | ||||
PREGNANCIES_COUNT_ECTOPIC | Wilcoxon test | N=0 | ||||
LYMPH_NODE_LOCATION | Kruskal-Wallis test | N=0 | ||||
LOCATION_OF_POSITIVE_MARGINS | Kruskal-Wallis test | N=2 | ||||
MENOPAUSE_STATUS | Kruskal-Wallis test | N=0 | ||||
LYMPHOVASCULAR_INVOLVEMENT | Wilcoxon test | N=0 | ||||
LYMPH_NODES_EXAMINED_HE_COUNT | Spearman correlation test | N=0 | ||||
LYMPH_NODES_EXAMINED | Spearman correlation test | N=0 | ||||
KERATINIZATION_SQUAMOUS_CELL | Wilcoxon test | N=0 | ||||
INITIAL_PATHOLOGIC_DX_YEAR | Spearman correlation test | N=0 | ||||
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Wilcoxon test | N=0 | ||||
HEIGHT_CM_AT_DIAGNOSIS | Spearman correlation test | N=0 | ||||
CORPUS_INVOLVEMENT | Wilcoxon test | N=0 | ||||
CERVIX_SUV_RESULTS | Spearman correlation test | N=0 | ||||
AJCC_TUMOR_PATHOLOGIC_PT | Kruskal-Wallis test | N=0 | ||||
AGE_AT_DIAGNOSIS | Spearman correlation test | N=0 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.5-177 (median=36.7) |
censored | N = 24 | |
death | N = 14 | |
Significant variables | N = 0 |
Table S2. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 46.95 (14) |
Significant variables | N = 0 |
Table S3. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 46.95 (14) |
Significant variables | N = 1 |
Table S4. Get Full Table List of one variable significantly correlated to 'AGE' by Linear regression analysis [lm (mutation rate ~ age)]. Compared to a correlation analysis testing for interdependence of the variables, a regression model attempts to describe the dependence of a variable on one (or more) explanatory variables assuming that there is a one-way causal effect from the explanatory variable(s) to the response variable. If 'Residuals vs Fitted' plot (a standard residual plot) shows a random pattern indicating a good fit for a linear model, it explains linear regression relationship between Mutation rate and age factor. Adj.R-squared (= Explained variation / Total variation) indicates regression model's explanatory power.
Adj.R.squared | F | P | Residual.std.err | DF | coef(intercept) | coef.p(intercept) | |
---|---|---|---|---|---|---|---|
MUTATIONRATE_NONSYNONYMOUS | 0.0789 | 4.17 | 0.0485 | 6.95e-06 | 36 | 1.7e-07 ( -2.59e-06 ) | 0.0485 ( 0.529 ) |
Table S5. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 1.26 (0.51) |
N | ||
1 | 24 | |
2 | 6 | |
3 | 1 | |
Significant variables | N = 0 |
Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Labels | N |
class0 | 17 | |
class1 | 15 | |
Significant variables | N = 0 |
Table S7. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 19 | |
MX | 13 | |
Significant variables | N = 0 |
Table S8. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
CERVICAL SQUAMOUS CELL CARCINOMA | 35 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 3 | |
Significant variables | N = 0 |
No variable related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S9. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 22 | |
YES | 16 | |
Significant variables | N = 0 |
Table S10. Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'
NUMBERPACKYEARSSMOKED | Mean (SD) | 18.43 (8) |
Significant variables | N = 0 |
Table S11. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1.42 (3) |
Significant variables | N = 0 |
Table S12. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
ASIAN | 1 | |
BLACK OR AFRICAN AMERICAN | 5 | |
WHITE | 32 | |
Significant variables | N = 0 |
Table S13. Basic characteristics of clinical feature: 'WEIGHT_KG_AT_DIAGNOSIS'
WEIGHT_KG_AT_DIAGNOSIS | Mean (SD) | 70.29 (14) |
Significant variables | N = 0 |
Table S14. Basic characteristics of clinical feature: 'TUMOR_STATUS'
TUMOR_STATUS | Labels | N |
TUMOR FREE | 22 | |
WITH TUMOR | 10 | |
Significant variables | N = 0 |
Table S15. Basic characteristics of clinical feature: 'NEOPLASMHISTOLOGICGRADE'
NEOPLASMHISTOLOGICGRADE | Labels | N |
G1 | 2 | |
G2 | 19 | |
G3 | 17 | |
Significant variables | N = 0 |
No variable related to 'TOBACCO_SMOKING_YEAR_STOPPED'.
Table S16. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_YEAR_STOPPED'
TOBACCO_SMOKING_YEAR_STOPPED | Mean (SD) | 1996.83 (5.7) |
Value | N | |
1988 | 1 | |
1995 | 2 | |
1997 | 1 | |
2003 | 2 | |
Significant variables | N = 0 |
No variable related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
Table S17. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Mean (SD) | 18.43 (8) |
Significant variables | N = 0 |
Table S18. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_HISTORY'
TOBACCO_SMOKING_HISTORY | Labels | N |
CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | 9 | |
CURRENT REFORMED SMOKER FOR > 15 YEARS | 2 | |
CURRENT SMOKER | 9 | |
LIFELONG NON-SMOKER | 17 | |
Significant variables | N = 0 |
No variable related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.
Table S19. Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'
PATIENT.AGEBEGANSMOKINGINYEARS | Mean (SD) | 20.45 (6.2) |
Significant variables | N = 0 |
Table S20. Basic characteristics of clinical feature: 'RADIATION_THERAPY_TYPE'
RADIATION_THERAPY_TYPE | Labels | N |
COMBINATION | 15 | |
EXTERNAL | 1 | |
EXTERNAL BEAM | 8 | |
Significant variables | N = 0 |
Table S21. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'
PREGNANCIES_COUNT_TOTAL | Mean (SD) | 3.14 (1.9) |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_STILLBIRTH'.
Table S22. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'
PREGNANCIES_COUNT_STILLBIRTH | Mean (SD) | 0.16 (0.58) |
Value | N | |
0 | 28 | |
1 | 2 | |
3 | 1 | |
Significant variables | N = 0 |
No variable related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.
Table S23. Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Mean (SD) | 0.33 (0.65) |
Value | N | |
0 | 25 | |
1 | 5 | |
2 | 3 | |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
Table S24. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_LIVE_BIRTH'
PREGNANCIES_COUNT_LIVE_BIRTH | Mean (SD) | 2.08 (1.3) |
Value | N | |
0 | 5 | |
1 | 7 | |
2 | 13 | |
3 | 4 | |
4 | 8 | |
Significant variables | N = 0 |
No variable related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.
Table S25. Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Mean (SD) | 0.68 (1) |
Value | N | |
0 | 20 | |
1 | 4 | |
2 | 4 | |
3 | 3 | |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_ECTOPIC'.
Table S26. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'
PREGNANCIES_COUNT_ECTOPIC | Labels | N |
class0 | 27 | |
class1 | 4 | |
Significant variables | N = 0 |
Table S27. Basic characteristics of clinical feature: 'LYMPH_NODE_LOCATION'
LYMPH_NODE_LOCATION | Labels | N |
2003 | 1 | |
2010 | 1 | |
COMMON ILIAC | 1 | |
PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR) | 12 | |
Significant variables | N = 0 |
2 variables related to 'LOCATION_OF_POSITIVE_MARGINS'.
Table S28. Basic characteristics of clinical feature: 'LOCATION_OF_POSITIVE_MARGINS'
LOCATION_OF_POSITIVE_MARGINS | Labels | N |
MICROSCOPIC PARAMETRIAL INVOLVEMENT | 4 | |
OTHER LOCATION, SPECIFY | 7 | |
POSITIVE VAGINAL MARGIN | 2 | |
Significant variables | N = 2 |
Table S29. Get Full Table List of 2 variables differentially expressed by 'LOCATION_OF_POSITIVE_MARGINS'
ANOVA_P | Q | |
---|---|---|
MUTATIONRATE_NONSYNONYMOUS | 0.02069 | 0.0388 |
MUTATIONRATE_SILENT | 0.01941 | 0.0388 |
Table S30. Basic characteristics of clinical feature: 'MENOPAUSE_STATUS'
MENOPAUSE_STATUS | Labels | N |
INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) | 2 | |
PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) | 1 | |
POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) | 13 | |
PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) | 19 | |
Significant variables | N = 0 |
No variable related to 'LYMPHOVASCULAR_INVOLVEMENT'.
Table S31. Basic characteristics of clinical feature: 'LYMPHOVASCULAR_INVOLVEMENT'
LYMPHOVASCULAR_INVOLVEMENT | Labels | N |
ABSENT | 9 | |
PRESENT | 21 | |
Significant variables | N = 0 |
No variable related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
Table S32. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED_HE_COUNT'
LYMPH_NODES_EXAMINED_HE_COUNT | Mean (SD) | 1.42 (3) |
Significant variables | N = 0 |
Table S33. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'
LYMPH_NODES_EXAMINED | Mean (SD) | 24.87 (14) |
Significant variables | N = 0 |
No variable related to 'KERATINIZATION_SQUAMOUS_CELL'.
Table S34. Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'
KERATINIZATION_SQUAMOUS_CELL | Labels | N |
KERATINIZING SQUAMOUS CELL CARCINOMA | 12 | |
NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 14 | |
Significant variables | N = 0 |
No variable related to 'INITIAL_PATHOLOGIC_DX_YEAR'.
Table S35. Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'
INITIAL_PATHOLOGIC_DX_YEAR | Mean (SD) | 2003.13 (5) |
Significant variables | N = 0 |
No variable related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.
Table S36. Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Labels | N |
FORMER USER | 9 | |
NEVER USED | 10 | |
Significant variables | N = 0 |
Table S37. Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'
HEIGHT_CM_AT_DIAGNOSIS | Mean (SD) | 162 (7.3) |
Significant variables | N = 0 |
Table S38. Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'
CORPUS_INVOLVEMENT | Labels | N |
ABSENT | 21 | |
PRESENT | 6 | |
Significant variables | N = 0 |
Table S39. Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'
CERVIX_SUV_RESULTS | Mean (SD) | 13.23 (4.5) |
Value | N | |
8.7 | 1 | |
9.95 | 1 | |
16.92 | 1 | |
17.36 | 1 | |
Significant variables | N = 0 |
No variable related to 'AJCC_TUMOR_PATHOLOGIC_PT'.
Table S40. Basic characteristics of clinical feature: 'AJCC_TUMOR_PATHOLOGIC_PT'
AJCC_TUMOR_PATHOLOGIC_PT | Labels | N |
T1B | 9 | |
T1B1 | 12 | |
T1B2 | 3 | |
T2 | 1 | |
T2A1 | 1 | |
T2B | 4 | |
T3B | 1 | |
TX | 1 | |
Significant variables | N = 0 |
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Expresson data file = CESC-TP.patients.counts_and_rates.txt
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Clinical data file = CESC-TP.merged_data.txt
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Number of patients = 38
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Number of variables = 2
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Number of clinical features = 39
For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R
For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R
For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
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.