This pipeline computes the correlation between APOBRC groups and selected clinical features.
Testing the association between APOBEC groups identified by 2 different apobec score and 45 clinical features across 194 patients, no significant finding detected with Q value < 0.25.
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3 subtypes identified in current cancer cohort by 'APOBEC MUTLOAD MINESTIMATE'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'APOBEC ENRICH'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
APOBEC MUTLOAD MINESTIMATE |
APOBEC ENRICH |
Time to Death | logrank test |
0.392 (0.967) |
0.0723 (0.651) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
0.0184 (0.29) |
0.456 (0.967) |
PATHOLOGY T STAGE | Fisher's exact test |
0.766 (0.967) |
0.737 (0.967) |
PATHOLOGY N STAGE | Fisher's exact test |
0.796 (0.967) |
0.724 (0.967) |
PATHOLOGY M STAGE | Fisher's exact test |
0.0456 (0.506) |
0.0874 (0.715) |
HISTOLOGICAL TYPE | Fisher's exact test |
0.0229 (0.295) |
0.0158 (0.29) |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test |
0.545 (0.967) |
0.673 (0.967) |
NUMBER PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.587 (0.967) |
0.682 (0.967) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.849 (0.967) |
0.669 (0.967) |
RACE | Fisher's exact test |
0.326 (0.967) |
0.24 (0.967) |
ETHNICITY | Fisher's exact test |
0.00721 (0.29) |
0.498 (0.967) |
WEIGHT KG AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.847 (0.967) |
0.912 (0.974) |
TUMOR STATUS | Fisher's exact test |
1 (1.00) |
0.745 (0.967) |
TUMOR SAMPLE PROCUREMENT COUNTRY | Fisher's exact test |
0.672 (0.967) |
0.242 (0.967) |
NEOPLASM HISTOLOGIC GRADE | Fisher's exact test |
0.542 (0.967) |
0.907 (0.974) |
TOBACCO SMOKING YEAR STOPPED | Kruskal-Wallis (anova) |
0.925 (0.974) |
0.429 (0.967) |
TOBACCO SMOKING PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.587 (0.967) |
0.682 (0.967) |
TOBACCO SMOKING HISTORY | Fisher's exact test |
0.93 (0.974) |
0.899 (0.974) |
PATIENT AGEBEGANSMOKINGINYEARS | Kruskal-Wallis (anova) |
0.306 (0.967) |
0.299 (0.967) |
RADIATION TOTAL DOSE | Kruskal-Wallis (anova) |
0.596 (0.967) |
0.803 (0.967) |
RADIATION THERAPY TYPE | Fisher's exact test |
0.497 (0.967) |
0.218 (0.967) |
RADIATION THERAPY STATUS | Fisher's exact test |
0.136 (0.939) |
1 (1.00) |
RADIATION THERAPY SITE | Fisher's exact test |
0.826 (0.967) |
0.325 (0.967) |
RADIATION ADJUVANT UNITS | Fisher's exact test |
0.215 (0.967) |
0.16 (0.967) |
PREGNANCIES COUNT TOTAL | Kruskal-Wallis (anova) |
0.447 (0.967) |
0.499 (0.967) |
PREGNANCIES COUNT STILLBIRTH | Kruskal-Wallis (anova) |
0.488 (0.967) |
0.757 (0.967) |
PATIENT PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Kruskal-Wallis (anova) |
0.732 (0.967) |
0.812 (0.967) |
PREGNANCIES COUNT LIVE BIRTH | Kruskal-Wallis (anova) |
0.402 (0.967) |
0.43 (0.967) |
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Kruskal-Wallis (anova) |
0.694 (0.967) |
0.848 (0.967) |
PREGNANCIES COUNT ECTOPIC | Kruskal-Wallis (anova) |
0.329 (0.967) |
0.39 (0.967) |
POS LYMPH NODE LOCATION | Fisher's exact test |
0.893 (0.974) |
0.791 (0.967) |
MENOPAUSE STATUS | Fisher's exact test |
0.00344 (0.29) |
0.0506 (0.506) |
LYMPHOVASCULAR INVOLVEMENT | Fisher's exact test |
0.765 (0.967) |
0.241 (0.967) |
LYMPH NODES EXAMINED HE COUNT | Kruskal-Wallis (anova) |
0.849 (0.967) |
0.669 (0.967) |
LYMPH NODES EXAMINED | Kruskal-Wallis (anova) |
0.694 (0.967) |
0.42 (0.967) |
KERATINIZATION SQUAMOUS CELL | Fisher's exact test |
0.216 (0.967) |
0.18 (0.967) |
INITIAL PATHOLOGIC DX YEAR | Kruskal-Wallis (anova) |
0.11 (0.829) |
0.0193 (0.29) |
HISTORY HORMONAL CONTRACEPTIVES USE | Fisher's exact test |
0.875 (0.974) |
0.481 (0.967) |
HEIGHT CM AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.381 (0.967) |
0.691 (0.967) |
CORPUS INVOLVEMENT | Fisher's exact test |
0.671 (0.967) |
0.606 (0.967) |
CHEMO CONCURRENT TYPE | Fisher's exact test |
0.521 (0.967) |
0.553 (0.967) |
CERVIX SUV RESULTS | Kruskal-Wallis (anova) | ||
AJCC TUMOR PATHOLOGIC PT | Fisher's exact test |
0.649 (0.967) |
0.615 (0.967) |
AGE AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.0117 (0.29) |
0.381 (0.967) |
STAGE EVENT CLINICAL STAGE | Fisher's exact test |
0.387 (0.967) |
0.226 (0.967) |
Cluster Labels | 0 | HIGH | LOW |
---|---|---|---|
Number of samples | 44 | 41 | 109 |
Cluster Labels | FC.HIGH.SIG | FC.LOW.NONSIG | FC.NEUTRAL |
---|---|---|---|
Number of samples | 144 | 40 | 10 |
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APOBEC groups file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/CESC-TP/15165229/APOBEC_clinical_corr_input_15168231/APOBEC_for_clinical.correlaion.input.categorical.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/15076797/CESC-TP.merged_data.txt
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Number of patients = 194
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Number of selected clinical features = 45
APOBEC classification based on APOBEC_MutLoad_MinEstimate : a. APOBEC non group -- samples with zero value, b. APOBEC hig group -- samples above median value in non zero samples, c. APOBEC hig group -- samples below median value in non zero samples.
APOBEC classification based on APOBEC_enrich : a. No Enrichmment group -- all samples with BH_Fisher_p-value_tCw >=0.05, b. Small enrichment group -- samples with BH_Fisher_p-value_tCw = < 0.05 and APOBEC_enrich=<2, c. High enrichment gruop -- samples with BH_Fisher_p-value_tCw =< 0.05 and APOBEC_enrich>2.
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.