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 13 clinical features across 395 patients, 8 significant findings detected with Q value < 0.25.
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3 subtypes identified in current cancer cohort by 'APOBEC MUTLOAD MINESTIMATE'. These subtypes correlate to 'Time to Death', 'GENDER', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
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3 subtypes identified in current cancer cohort by 'APOBEC ENRICH'. These subtypes correlate to 'Time to Death', 'RADIATION_THERAPY', and 'RACE'.
Clinical Features |
Statistical Tests |
APOBEC MUTLOAD MINESTIMATE |
APOBEC ENRICH |
Time to Death | logrank test |
0.000892 (0.00773) |
0.0188 (0.092) |
YEARS TO BIRTH | Kruskal-Wallis (anova) |
0.637 (0.772) |
0.611 (0.772) |
PATHOLOGIC STAGE | Fisher's exact test |
0.121 (0.337) |
0.365 (0.635) |
PATHOLOGY T STAGE | Fisher's exact test |
0.381 (0.635) |
0.135 (0.337) |
PATHOLOGY N STAGE | Fisher's exact test |
0.143 (0.337) |
0.552 (0.755) |
PATHOLOGY M STAGE | Fisher's exact test |
0.907 (0.982) |
0.216 (0.468) |
GENDER | Fisher's exact test |
0.0248 (0.092) |
0.653 (0.772) |
RADIATION THERAPY | Fisher's exact test |
0.0227 (0.092) |
0.00376 (0.0244) |
KARNOFSKY PERFORMANCE SCORE | Kruskal-Wallis (anova) |
0.808 (0.914) |
0.488 (0.704) |
NUMBER PACK YEARS SMOKED | Kruskal-Wallis (anova) |
0.39 (0.635) |
0.391 (0.635) |
NUMBER OF LYMPH NODES | Kruskal-Wallis (anova) |
0.0501 (0.163) |
0.454 (0.695) |
RACE | Fisher's exact test |
0.00022 (0.00286) |
4e-05 (0.00104) |
ETHNICITY | Fisher's exact test |
1 (1.00) |
1 (1.00) |
Cluster Labels | 0 | HIGH | LOW |
---|---|---|---|
Number of samples | 46 | 172 | 177 |
P value = 0.000892 (logrank test), Q value = 0.0077
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 392 | 175 | 0.6 - 166.0 (17.6) |
0 | 45 | 27 | 2.0 - 93.0 (13.6) |
HIGH | 171 | 62 | 0.6 - 166.0 (19.8) |
LOW | 176 | 86 | 0.6 - 165.7 (16.1) |
P value = 0.0248 (Fisher's exact test), Q value = 0.092
nPatients | FEMALE | MALE |
---|---|---|
ALL | 102 | 293 |
0 | 13 | 33 |
HIGH | 33 | 139 |
LOW | 56 | 121 |
P value = 0.0227 (Fisher's exact test), Q value = 0.092
nPatients | NO | YES |
---|---|---|
ALL | 350 | 20 |
0 | 35 | 6 |
HIGH | 156 | 5 |
LOW | 159 | 9 |
P value = 0.0501 (Kruskal-Wallis (anova)), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 288 | 1.8 (4.4) |
0 | 29 | 0.9 (1.7) |
HIGH | 128 | 1.7 (4.8) |
LOW | 131 | 2.1 (4.3) |
P value = 0.00022 (Fisher's exact test), Q value = 0.0029
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 39 | 22 | 317 |
0 | 13 | 4 | 27 |
HIGH | 9 | 7 | 150 |
LOW | 17 | 11 | 140 |
Cluster Labels | FC.HIGH.ENRICH | FC.LOW.ENRICH | FC.NO.ENRICH |
---|---|---|---|
Number of samples | 327 | 22 | 46 |
P value = 0.0188 (logrank test), Q value = 0.092
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 392 | 175 | 0.6 - 166.0 (17.6) |
FC.HIGH.ENRICH | 325 | 137 | 0.6 - 166.0 (17.9) |
FC.LOW.ENRICH | 22 | 11 | 1.9 - 52.0 (13.7) |
FC.NO.ENRICH | 45 | 27 | 2.0 - 93.0 (13.6) |
P value = 0.00376 (Fisher's exact test), Q value = 0.024
nPatients | NO | YES |
---|---|---|
ALL | 350 | 20 |
FC.HIGH.ENRICH | 297 | 11 |
FC.LOW.ENRICH | 18 | 3 |
FC.NO.ENRICH | 35 | 6 |
P value = 4e-05 (Fisher's exact test), Q value = 0.001
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 39 | 22 | 317 |
FC.HIGH.ENRICH | 22 | 16 | 276 |
FC.LOW.ENRICH | 4 | 2 | 14 |
FC.NO.ENRICH | 13 | 4 | 27 |
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APOBEC groups file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BLCA-TP/22506785/APOBEC_clinical_corr_input_22536864/APOBEC_for_clinical.correlaion.input.categorical.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt
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Number of patients = 395
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Number of selected clinical features = 13
APOBEC classification based on APOBEC_MutLoad_MinEstimate : a. APOBEC non group -- samples with zero value, b. APOBEC high group -- samples above median value in non zero samples, c. APOBEC low 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. Low enrichment group -- samples with BH_Fisher_p-value_tCw = < 0.05 and APOBEC_enrich=<2, c. High enrichment group -- 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.