This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 166 genes and 5 clinical features across 200 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
-
16 genes correlated to 'HISTOLOGICAL.TYPE'.
-
TP53|P53-R-V , CHEK2|CHK2_PT68-R-C , AKT1 AKT2 AKT3|AKT_PS473-R-V , PGR|PR-R-V , CDC2|CDK1-R-V , ...
-
1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
CHEK1|CHK1_PS345-R-C
-
No genes correlated to 'Time to Death', 'AGE', and 'NEOADJUVANT.THERAPY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=16 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=1 | yes | N=1 | no | N=0 |
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0-173.6 (median=21.7) |
censored | N = 187 | |
death | N = 13 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.73 (11) |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 164 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | 3 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | 3 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | 4 | |
MIXED SEROUS AND ENDOMETRIOID | 3 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 23 | |
Significant markers | N = 16 |
ANOVA_P | Q | |
---|---|---|
TP53|P53-R-V | 7.144e-12 | 1.19e-09 |
CHEK2|CHK2_PT68-R-C | 7.824e-09 | 1.29e-06 |
AKT1 AKT2 AKT3|AKT_PS473-R-V | 6.908e-08 | 1.13e-05 |
PGR|PR-R-V | 1.307e-07 | 2.13e-05 |
CDC2|CDK1-R-V | 2.576e-07 | 4.17e-05 |
CDH1|E-CADHERIN-R-V | 2.644e-07 | 4.26e-05 |
ESR1|ER-ALPHA-R-V | 9.567e-07 | 0.000153 |
ESR1|ER-ALPHA_PS118-R-V | 3.992e-06 | 0.000635 |
EEF2|EEF2-R-V | 7.75e-06 | 0.00122 |
EIF4EBP1|4E-BP1_PS65-R-V | 1.874e-05 | 0.00294 |
One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 80 | |
YES | 120 | |
Significant markers | N = 1 | |
Higher in YES | 1 | |
Higher in NO | 0 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
CHEK1|CHK1_PS345-R-C | 3.69 | 0.0002956 | 0.0491 | 0.631 |
-
Expresson data file = UCEC.rppa.txt
-
Clinical data file = UCEC.clin.merged.picked.txt
-
Number of patients = 200
-
Number of genes = 166
-
Number of clinical features = 5
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 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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.