This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.
Testing the association between 2 variables and 45 clinical features across 194 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one variables.
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2 variables correlated to 'AGE'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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2 variables correlated to 'AGE_mutation.rate'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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2 variables correlated to 'NUMBERPACKYEARSSMOKED'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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2 variables correlated to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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2 variables correlated to 'MENOPAUSE_STATUS'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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1 variable correlated to 'KERATINIZATION_SQUAMOUS_CELL'.
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MUTATIONRATE_SILENT
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1 variable correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.
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MUTATIONRATE_SILENT
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2 variables correlated to 'AGE_AT_DIAGNOSIS'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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No variables correlated to 'Time to Death', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBER.OF.LYMPH.NODES', 'RACE', 'ETHNICITY', 'WEIGHT_KG_AT_DIAGNOSIS', 'TUMOR_STATUS', 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_TOTAL_DOSE', 'RADIATION_THERAPY_TYPE', 'RADIATION_THERAPY_STATUS', 'RADIATION_THERAPY_SITE', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', 'CERVIX_SUV_RESULTS', 'AJCC_TUMOR_PATHOLOGIC_PT', and 'STAGE_EVENT.CLINICAL_STAGE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant variables | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=2 | older | N=2 | younger | N=0 |
AGE | Linear Regression Analysis | N=2 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=2 | higher numberpackyearssmoked | N=2 | lower numberpackyearssmoked | N=0 |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 | ||||
WEIGHT_KG_AT_DIAGNOSIS | Spearman correlation test | N=0 | ||||
TUMOR_STATUS | Wilcoxon test | N=0 | ||||
TUMOR_SAMPLE_PROCUREMENT_COUNTRY | Kruskal-Wallis 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=2 | higher tobacco_smoking_pack_years_smoked | N=2 | lower tobacco_smoking_pack_years_smoked | N=0 |
TOBACCO_SMOKING_HISTORY | Kruskal-Wallis test | N=0 | ||||
PATIENT AGEBEGANSMOKINGINYEARS | Spearman correlation test | N=0 | ||||
RADIATION_TOTAL_DOSE | Spearman correlation test | N=0 | ||||
RADIATION_THERAPY_TYPE | Kruskal-Wallis test | N=0 | ||||
RADIATION_THERAPY_STATUS | Wilcoxon test | N=0 | ||||
RADIATION_THERAPY_SITE | 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 | Spearman correlation test | N=0 | ||||
POS_LYMPH_NODE_LOCATION | Kruskal-Wallis test | N=0 | ||||
MENOPAUSE_STATUS | Kruskal-Wallis test | N=2 | ||||
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=1 | non-keratinizing squamous cell carcinoma | N=1 | keratinizing squamous cell carcinoma | N=0 |
INITIAL_PATHOLOGIC_DX_YEAR | Spearman correlation test | N=1 | higher initial_pathologic_dx_year | N=0 | lower initial_pathologic_dx_year | N=1 |
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Kruskal-Wallis test | N=0 | ||||
HEIGHT_CM_AT_DIAGNOSIS | Spearman correlation test | N=0 | ||||
CORPUS_INVOLVEMENT | Wilcoxon test | N=0 | ||||
CHEMO_CONCURRENT_TYPE | Kruskal-Wallis 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=2 | higher age_at_diagnosis | N=2 | lower age_at_diagnosis | N=0 |
STAGE_EVENT CLINICAL_STAGE | Kruskal-Wallis test | N=0 |
Time to Death | Duration (Months) | 0-195.8 (median=15) |
censored | N = 152 | |
death | N = 37 | |
Significant variables | N = 0 |
AGE | Mean (SD) | 47.25 (13) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
AGE | Mean (SD) | 47.25 (13) |
Significant variables | N = 2 |
PATHOLOGY.T.STAGE | Mean (SD) | 1.34 (0.59) |
N | ||
1 | 106 | |
2 | 40 | |
3 | 3 | |
4 | 2 | |
Significant variables | N = 0 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 95 | |
class1 | 46 | |
Significant variables | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 81 | |
M1 | 4 | |
MX | 70 | |
Significant variables | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ADENOSQUAMOUS | 4 | |
CERVICAL SQUAMOUS CELL CARCINOMA | 158 | |
ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | 5 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 22 | |
ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | 2 | |
MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE | 3 | |
Significant variables | N = 0 |
No variable related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 32 | |
YES | 162 | |
Significant variables | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 18.65 (12) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1.02 (2.2) |
Significant variables | N = 0 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 8 | |
ASIAN | 19 | |
BLACK OR AFRICAN AMERICAN | 16 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 1 | |
WHITE | 138 | |
Significant variables | N = 0 |
ETHNICITY | Labels | N |
HISPANIC OR LATINO | 14 | |
NOT HISPANIC OR LATINO | 134 | |
Significant variables | N = 0 |
WEIGHT_KG_AT_DIAGNOSIS | Mean (SD) | 75.98 (22) |
Significant variables | N = 0 |
TUMOR_STATUS | Labels | N |
TUMOR FREE | 72 | |
WITH TUMOR | 26 | |
Significant variables | N = 0 |
No variable related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.
TUMOR_SAMPLE_PROCUREMENT_COUNTRY | Labels | N |
CANADA | 5 | |
RUSSIA | 10 | |
UKRAINE | 6 | |
UNITED STATES | 159 | |
VIETNAM | 14 | |
Significant variables | N = 0 |
NEOPLASMHISTOLOGICGRADE | Labels | N |
G1 | 14 | |
G2 | 88 | |
G3 | 82 | |
G4 | 1 | |
GX | 8 | |
Significant variables | N = 0 |
No variable related to 'TOBACCO_SMOKING_YEAR_STOPPED'.
TOBACCO_SMOKING_YEAR_STOPPED | Mean (SD) | 1998.93 (12) |
Significant variables | N = 0 |
2 variables related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Mean (SD) | 18.65 (12) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
TOBACCO_SMOKING_HISTORY | Labels | N |
CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | 26 | |
CURRENT REFORMED SMOKER FOR > 15 YEARS | 8 | |
CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED | 1 | |
CURRENT SMOKER | 37 | |
LIFELONG NON-SMOKER | 92 | |
Significant variables | N = 0 |
No variable related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.
PATIENT.AGEBEGANSMOKINGINYEARS | Mean (SD) | 21.37 (7.4) |
Significant variables | N = 0 |
RADIATION_TOTAL_DOSE | Mean (SD) | 3863.29 (1700) |
Significant variables | N = 0 |
RADIATION_THERAPY_TYPE | Labels | N |
COMBINATION | 20 | |
EXTERNAL | 45 | |
EXTERNAL BEAM | 12 | |
IMPLANTS | 1 | |
INTERNAL | 6 | |
Significant variables | N = 0 |
No variable related to 'RADIATION_THERAPY_STATUS'.
RADIATION_THERAPY_STATUS | Labels | N |
COMPLETED AS PLANNED | 26 | |
TREATMENT NOT COMPLETED | 3 | |
Significant variables | N = 0 |
RADIATION_THERAPY_SITE | Labels | N |
DISTANT RECURRENCE | 2 | |
LOCAL RECURRENCE | 2 | |
PRIMARY TUMOR FIELD | 15 | |
REGIONAL SITE | 3 | |
Significant variables | N = 0 |
PREGNANCIES_COUNT_TOTAL | Mean (SD) | 3.41 (2.4) |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_STILLBIRTH'.
PREGNANCIES_COUNT_STILLBIRTH | Mean (SD) | 0.08 (0.37) |
Value | N | |
0 | 95 | |
1 | 5 | |
3 | 1 | |
Significant variables | N = 0 |
No variable related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Mean (SD) | 0.31 (0.57) |
Value | N | |
0 | 81 | |
1 | 25 | |
2 | 3 | |
3 | 1 | |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
PREGNANCIES_COUNT_LIVE_BIRTH | Mean (SD) | 2.4 (1.7) |
Significant variables | N = 0 |
No variable related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Mean (SD) | 0.88 (1.9) |
Significant variables | N = 0 |
No variable related to 'PREGNANCIES_COUNT_ECTOPIC'.
PREGNANCIES_COUNT_ECTOPIC | Mean (SD) | 0.11 (0.34) |
Value | N | |
0 | 93 | |
1 | 9 | |
2 | 1 | |
Significant variables | N = 0 |
POS_LYMPH_NODE_LOCATION | Labels | N |
MACROSCOPIC PARAMETRIAL INVOLVEMENT | 2 | |
MICROSCOPIC PARAMETRIAL INVOLVEMENT | 6 | |
OTHER LOCATION, SPECIFY | 26 | |
POSITIVE BLADDER MARGIN | 1 | |
POSITIVE VAGINAL MARGIN | 6 | |
Significant variables | N = 0 |
MENOPAUSE_STATUS | Labels | N |
INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) | 2 | |
PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) | 10 | |
POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) | 60 | |
PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) | 88 | |
Significant variables | N = 2 |
No variable related to 'LYMPHOVASCULAR_INVOLVEMENT'.
LYMPHOVASCULAR_INVOLVEMENT | Labels | N |
ABSENT | 63 | |
PRESENT | 67 | |
Significant variables | N = 0 |
No variable related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
LYMPH_NODES_EXAMINED_HE_COUNT | Mean (SD) | 1.02 (2.2) |
Significant variables | N = 0 |
LYMPH_NODES_EXAMINED | Mean (SD) | 21.53 (13) |
Significant variables | N = 0 |
One variable related to 'KERATINIZATION_SQUAMOUS_CELL'.
KERATINIZATION_SQUAMOUS_CELL | Labels | N |
KERATINIZING SQUAMOUS CELL CARCINOMA | 39 | |
NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 86 | |
Significant variables | N = 1 | |
Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 1 | |
Higher in KERATINIZING SQUAMOUS CELL CARCINOMA | 0 |
W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
MUTATIONRATE_SILENT | 1283.5 | 0.0362 | 0.0724 | 0.6173 |
One variable related to 'INITIAL_PATHOLOGIC_DX_YEAR'.
INITIAL_PATHOLOGIC_DX_YEAR | Mean (SD) | 2007.67 (5.1) |
Significant variables | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MUTATIONRATE_SILENT | -0.1527 | 0.03452 | 0.069 |
No variable related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Labels | N |
CURRENT USER | 8 | |
FORMER USER | 43 | |
NEVER USED | 46 | |
Significant variables | N = 0 |
HEIGHT_CM_AT_DIAGNOSIS | Mean (SD) | 162.15 (6.6) |
Significant variables | N = 0 |
CORPUS_INVOLVEMENT | Labels | N |
ABSENT | 88 | |
PRESENT | 16 | |
Significant variables | N = 0 |
CHEMO_CONCURRENT_TYPE | Labels | N |
CARBOPLATIN | 2 | |
CISPLATIN | 16 | |
OTHER | 1 | |
Significant variables | N = 0 |
CERVIX_SUV_RESULTS | Mean (SD) | 11.79 (3.8) |
Significant variables | N = 0 |
No variable related to 'AJCC_TUMOR_PATHOLOGIC_PT'.
AJCC_TUMOR_PATHOLOGIC_PT | Labels | N |
T1A | 1 | |
T1A1 | 1 | |
T1B | 23 | |
T1B1 | 59 | |
T1B2 | 22 | |
T2 | 4 | |
T2A | 7 | |
T2A1 | 6 | |
T2A2 | 10 | |
T2B | 13 | |
T3 | 1 | |
T3B | 2 | |
T4 | 2 | |
TX | 9 | |
Significant variables | N = 0 |
AGE_AT_DIAGNOSIS | Mean (SD) | 47.42 (13) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
No variable related to 'STAGE_EVENT.CLINICAL_STAGE'.
STAGE_EVENT.CLINICAL_STAGE | Labels | N |
STAGE I | 4 | |
STAGE IA | 2 | |
STAGE IA1 | 1 | |
STAGE IA2 | 1 | |
STAGE IB | 28 | |
STAGE IB1 | 52 | |
STAGE IB2 | 29 | |
STAGE II | 4 | |
STAGE IIA | 6 | |
STAGE IIA1 | 5 | |
STAGE IIA2 | 7 | |
STAGE IIB | 14 | |
STAGE III | 1 | |
STAGE IIIB | 29 | |
STAGE IVA | 2 | |
STAGE IVB | 5 | |
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 = 194
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Number of variables = 2
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Number of clinical features = 45
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.