This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18566 genes and 5 clinical features across 263 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.
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1 gene correlated to 'Time to Death'.
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KRTCAP3|200634
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56 genes correlated to 'AGE'.
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STS|412 , LRP6|4040 , C8ORF55|51337 , EIF4E3|317649 , PDHA1|5160 , ...
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1 gene correlated to 'TUMOR.STAGE'.
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BACE1|23621
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No genes correlated to '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 | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=1 | shorter survival | N=0 | longer survival | N=1 |
AGE | Spearman correlation test | N=56 | older | N=30 | 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 |
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0.3-180.2 (median=28.2) |
censored | N = 114 | |
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 | 7.03e-07 | 0.013 | 0.399 |
AGE | Mean (SD) | 59.06 (11) |
Significant markers | N = 56 | |
pos. correlated | 30 | |
neg. correlated | 26 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
STS|412 | -0.3996 | 3.117e-11 | 5.79e-07 |
LRP6|4040 | 0.3592 | 3.268e-09 | 6.07e-05 |
C8ORF55|51337 | -0.3585 | 3.519e-09 | 6.53e-05 |
EIF4E3|317649 | -0.3552 | 4.985e-09 | 9.25e-05 |
PDHA1|5160 | -0.3489 | 9.635e-09 | 0.000179 |
C12ORF4|57102 | 0.3472 | 1.15e-08 | 0.000213 |
GREB1|9687 | -0.3456 | 1.362e-08 | 0.000253 |
APPL2|55198 | 0.3397 | 2.466e-08 | 0.000458 |
ADAM15|8751 | -0.3394 | 2.556e-08 | 0.000474 |
DEPDC6|64798 | -0.3373 | 3.152e-08 | 0.000585 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 74.67 (12) |
Score | N | |
60 | 5 | |
80 | 9 | |
100 | 1 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 3.06 (0.44) |
N | ||
Stage 2 | 18 | |
Stage 3 | 211 | |
Stage 4 | 33 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
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BACE1|23621 | 0.2981 | 8.941e-07 | 0.0166 |
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Expresson data file = OV.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = OV.clin.merged.picked.txt
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Number of patients = 263
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Number of genes = 18566
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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.