(primary solid tumor cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18559 genes and 4 clinical features across 262 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.
-
1 gene correlated to 'Time to Death'.
-
KRTCAP3|200634
-
55 genes correlated to 'AGE'.
-
STS|412 , LRP6|4040 , EIF4E3|317649 , C8ORF55|51337 , PDHA1|5160 , ...
-
1 gene correlated to 'TUMOR.STAGE'.
-
BACE1|23621
-
No genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'
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=1 | shorter survival | N=0 | longer survival | N=1 |
AGE | Spearman correlation test | N=55 | older | N=29 | younger | N=26 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=1 | higher stage | N=1 | lower stage | N=0 |
Time to Death | Duration (Months) | 0.3-180.2 (median=28) |
censored | N = 113 | |
death | N = 147 | |
Significant markers | N = 1 | |
associated with shorter survival | 0 | |
associated with longer survival | 1 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
KRTCAP3|200634 | 0.68 | 1.938e-06 | 0.036 | 0.402 |
AGE | Mean (SD) | 59.02 (11) |
Significant markers | N = 55 | |
pos. correlated | 29 | |
neg. correlated | 26 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
STS|412 | -0.396 | 5.253e-11 | 9.75e-07 |
LRP6|4040 | 0.364 | 2.08e-09 | 3.86e-05 |
EIF4E3|317649 | -0.3599 | 3.234e-09 | 6e-05 |
C8ORF55|51337 | -0.3596 | 3.343e-09 | 6.2e-05 |
PDHA1|5160 | -0.3515 | 7.933e-09 | 0.000147 |
APPL2|55198 | 0.3455 | 1.466e-08 | 0.000272 |
C12ORF4|57102 | 0.3435 | 1.789e-08 | 0.000332 |
GREB1|9687 | -0.3418 | 2.124e-08 | 0.000394 |
ADAM15|8751 | -0.3411 | 2.29e-08 | 0.000425 |
NLK|51701 | 0.3408 | 2.351e-08 | 0.000436 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 74.29 (12) |
Score | N | |
60 | 5 | |
80 | 8 | |
100 | 1 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 3.06 (0.44) |
N | ||
Stage 2 | 18 | |
Stage 3 | 210 | |
Stage 4 | 33 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
BACE1|23621 | 0.2983 | 9.229e-07 | 0.0171 |
-
Expresson data file = OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Clinical data file = OV-TP.clin.merged.picked.txt
-
Number of patients = 262
-
Number of genes = 18559
-
Number of clinical features = 4
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 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.