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 39 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 |
0.331 (1.00) |
0.129 (0.664) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
0.0215 (0.277) |
0.581 (1.00) |
PATHOLOGY T STAGE | Fisher's exact test |
0.758 (1.00) |
0.891 (1.00) |
PATHOLOGY N STAGE | Fisher's exact test |
0.827 (1.00) |
0.952 (1.00) |
PATHOLOGY M STAGE | Fisher's exact test |
0.0252 (0.277) |
0.0611 (0.476) |
RADIATION THERAPY | Fisher's exact test |
0.768 (1.00) |
0.404 (1.00) |
HISTOLOGICAL TYPE | Fisher's exact test |
0.0284 (0.277) |
0.0146 (0.254) |
NUMBER PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.442 (1.00) |
0.667 (1.00) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.899 (1.00) |
0.924 (1.00) |
RACE | Fisher's exact test |
0.386 (1.00) |
0.465 (1.00) |
ETHNICITY | Fisher's exact test |
0.0163 (0.254) |
0.563 (1.00) |
WEIGHT KG AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.42 (1.00) |
0.972 (1.00) |
TUMOR STATUS | Fisher's exact test |
0.943 (1.00) |
0.802 (1.00) |
NEOPLASM HISTOLOGIC GRADE | Fisher's exact test |
0.322 (1.00) |
0.928 (1.00) |
TOBACCO SMOKING YEAR STOPPED | Kruskal-Wallis (anova) |
0.388 (1.00) |
0.232 (0.953) |
TOBACCO SMOKING PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.442 (1.00) |
0.667 (1.00) |
TOBACCO SMOKING HISTORY | Fisher's exact test |
0.882 (1.00) |
0.871 (1.00) |
AGEBEGANSMOKINGINYEARS | Kruskal-Wallis (anova) |
0.265 (1.00) |
0.274 (1.00) |
RADIATION THERAPY STATUS | Fisher's exact test |
0.136 (0.664) |
1 (1.00) |
PREGNANCIES COUNT TOTAL | Kruskal-Wallis (anova) |
0.757 (1.00) |
0.674 (1.00) |
PREGNANCIES COUNT STILLBIRTH | Kruskal-Wallis (anova) |
0.598 (1.00) |
0.716 (1.00) |
PREGNANCY SPONTANEOUS ABORTION COUNT | Kruskal-Wallis (anova) |
0.655 (1.00) |
0.665 (1.00) |
PREGNANCIES COUNT LIVE BIRTH | Kruskal-Wallis (anova) |
0.708 (1.00) |
0.539 (1.00) |
PREGNANCY THERAPEUTIC ABORTION COUNT | Kruskal-Wallis (anova) |
0.677 (1.00) |
0.825 (1.00) |
PREGNANCIES COUNT ECTOPIC | Kruskal-Wallis (anova) |
0.369 (1.00) |
0.328 (1.00) |
POS LYMPH NODE LOCATION | Fisher's exact test |
0.926 (1.00) |
0.91 (1.00) |
MENOPAUSE STATUS | Fisher's exact test |
0.00445 (0.254) |
0.13 (0.664) |
LYMPHOVASCULAR INVOLVEMENT | Fisher's exact test |
0.794 (1.00) |
0.401 (1.00) |
LYMPH NODES EXAMINED HE COUNT | Kruskal-Wallis (anova) |
0.899 (1.00) |
0.924 (1.00) |
LYMPH NODES EXAMINED | Kruskal-Wallis (anova) |
0.895 (1.00) |
0.607 (1.00) |
KERATINIZATION SQUAMOUS CELL | Fisher's exact test |
0.163 (0.748) |
0.186 (0.807) |
INITIAL PATHOLOGIC DX YEAR | Kruskal-Wallis (anova) |
0.0575 (0.476) |
0.0113 (0.254) |
HISTORY HORMONAL CONTRACEPTIVES USE | Fisher's exact test |
0.782 (1.00) |
0.349 (1.00) |
HEIGHT CM AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.474 (1.00) |
0.773 (1.00) |
CORPUS INVOLVEMENT | Fisher's exact test |
0.77 (1.00) |
0.562 (1.00) |
CHEMO CONCURRENT TYPE | Fisher's exact test |
0.0826 (0.586) |
0.136 (0.664) |
CERVIX SUV RESULTS | Kruskal-Wallis (anova) | ||
AGE AT DIAGNOSIS | Kruskal-Wallis (anova) |
0.0147 (0.254) |
0.519 (1.00) |
CLINICAL STAGE | Fisher's exact test |
0.294 (1.00) |
0.128 (0.664) |
Cluster Labels | 0 | HIGH | LOW |
---|---|---|---|
Number of samples | 46 | 43 | 105 |
Cluster Labels | FC.HIGH.SIG | FC.LOW.NONSIG | FC.NEUTRAL |
---|---|---|---|
Number of samples | 141 | 40 | 13 |
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APOBEC groups file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/CESC-TP/20063368/APOBEC_clinical_corr_input_20063466/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/19775059/CESC-TP.merged_data.txt
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Number of patients = 194
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Number of selected clinical features = 39
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.