This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18892 genes and 5 clinical features across 297 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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71 genes correlated to 'AGE'.
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C8ORF55|51337_CALCULATED , GREB1|9687_CALCULATED , DEPDC6|64798_CALCULATED , STS|412_CALCULATED , EIF4E3|317649_CALCULATED , ...
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1 gene correlated to 'TUMOR.STAGE'.
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BACE1|23621_CALCULATED
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No genes correlated to 'Time to Death', 'KARNOFSKY.PERFORMANCE.SCORE', and 'NEOADJUVANT.THERAPY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=71 | older | N=27 | younger | N=44 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=1 | higher stage | N=1 | lower stage | N=0 |
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0.3-180.2 (median=28.3) |
censored | N = 126 | |
death | N = 169 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 59.21 (11) |
Significant markers | N = 71 | |
pos. correlated | 27 | |
neg. correlated | 44 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
C8ORF55|51337_CALCULATED | -0.3516 | 7.779e-10 | 1.47e-05 |
GREB1|9687_CALCULATED | -0.3483 | 1.145e-09 | 2.16e-05 |
DEPDC6|64798_CALCULATED | -0.348 | 1.187e-09 | 2.24e-05 |
STS|412_CALCULATED | -0.3464 | 1.439e-09 | 2.72e-05 |
EIF4E3|317649_CALCULATED | -0.3463 | 1.448e-09 | 2.74e-05 |
ADAM15|8751_CALCULATED | -0.3454 | 1.606e-09 | 3.03e-05 |
PDHA1|5160_CALCULATED | -0.3453 | 1.623e-09 | 3.06e-05 |
GALNT4|8693_CALCULATED | -0.332 | 7.25e-09 | 0.000137 |
C9ORF103|414328_CALCULATED | -0.3236 | 1.812e-08 | 0.000342 |
TIGD5|84948_CALCULATED | -0.3217 | 2.217e-08 | 0.000419 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 76.25 (13) |
Score | N | |
60 | 5 | |
80 | 9 | |
100 | 2 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 3.06 (0.42) |
N | ||
Stage 2 | 18 | |
Stage 3 | 241 | |
Stage 4 | 36 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
BACE1|23621_CALCULATED | 0.2993 | 1.607e-07 | 0.00304 |
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Expresson data file = OV.mRNAseq_RPKM_log2.txt
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Clinical data file = OV.clin.merged.picked.txt
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Number of patients = 297
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Number of genes = 18892
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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 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.