This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18296 genes and 7 clinical features across 88 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.
-
11 genes correlated to 'GENDER'.
-
USP9Y|8287 , PRKY|5616 , ZFY|7544 , XIST|7503 , RPS4Y1|6192 , ...
-
No genes correlated to 'Time to Death', 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'NUMBERPACKYEARSSMOKED', 'STOPPEDSMOKINGYEAR', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
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 | ||||
GENDER | t test | N=11 | male | N=9 | female | N=2 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
STOPPEDSMOKINGYEAR | Spearman correlation test | N=0 | ||||
TOBACCOSMOKINGHISTORYINDICATOR | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.4-118.9 (median=7.2) |
censored | N = 58 | |
death | N = 25 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 66.61 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 27 | |
MALE | 61 | |
Significant markers | N = 11 | |
Higher in MALE | 9 | |
Higher in FEMALE | 2 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
USP9Y|8287 | 29.12 | 4.314e-37 | 7.89e-33 | 1 |
PRKY|5616 | 21.36 | 5.467e-33 | 9.99e-29 | 0.998 |
ZFY|7544 | 27.01 | 6.007e-29 | 1.1e-24 | 1 |
XIST|7503 | -17.66 | 1.127e-26 | 2.06e-22 | 0.9901 |
RPS4Y1|6192 | 33.02 | 5.838e-26 | 1.07e-21 | 1 |
TSIX|9383 | -12.97 | 8.321e-18 | 1.52e-13 | 0.9769 |
NLGN4Y|22829 | 14.46 | 5.861e-17 | 1.07e-12 | 0.9826 |
DDX3Y|8653 | 25.73 | 1.933e-16 | 3.53e-12 | 1 |
CYORF15A|246126 | 22.15 | 1.54e-15 | 2.81e-11 | 1 |
KDM5D|8284 | 29.81 | 9.224e-15 | 1.69e-10 | 1 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 78 (18) |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 34.41 (23) |
Significant markers | N = 0 |
STOPPEDSMOKINGYEAR | Mean (SD) | 1990.62 (19) |
Significant markers | N = 0 |
-
Expresson data file = BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 88
-
Number of genes = 18296
-
Number of clinical features = 7
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 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.