This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 12042 genes and 6 clinical features across 519 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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21 genes correlated to 'Time to Death'.
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CLEC5A , EFEMP2 , NCOA4 , ATP5C1 , DIRAS3 , ...
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76 genes correlated to 'AGE'.
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RANBP17 , FBXO17 , TUSC3 , KIAA0495 , NOL3 , ...
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23 genes correlated to 'GENDER'.
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DDX3Y , RPS4Y1 , EIF1AY , JARID1D , NLGN4Y , ...
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1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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NPAT
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8 genes correlated to 'NEOADJUVANT.THERAPY'.
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WDR57 , SSNA1 , SMU1 , DNAJA2 , IDH3A , ...
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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=21 | shorter survival | N=11 | longer survival | N=10 |
AGE | Spearman correlation test | N=76 | older | N=42 | younger | N=34 |
GENDER | t test | N=23 | male | N=11 | female | N=12 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=1 | yes | N=0 | no | N=1 |
NEOADJUVANT THERAPY | t test | N=8 | yes | N=0 | no | N=8 |
Time to Death | Duration (Months) | 0.1-127.6 (median=9.9) |
censored | N = 116 | |
death | N = 403 | |
Significant markers | N = 21 | |
associated with shorter survival | 11 | |
associated with longer survival | 10 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
CLEC5A | 1.23 | 7.107e-08 | 0.00086 | 0.584 |
EFEMP2 | 1.3 | 7.708e-08 | 0.00093 | 0.542 |
NCOA4 | 0.56 | 8.196e-08 | 0.00099 | 0.442 |
ATP5C1 | 0.59 | 8.228e-08 | 0.00099 | 0.451 |
DIRAS3 | 1.22 | 1.111e-07 | 0.0013 | 0.558 |
RANBP17 | 0.46 | 1.833e-07 | 0.0022 | 0.427 |
ANKRD26 | 0.39 | 2.458e-07 | 0.003 | 0.446 |
HIST3H2A | 0.82 | 3.552e-07 | 0.0043 | 0.427 |
ZIC3 | 0.48 | 6.625e-07 | 0.008 | 0.444 |
FZD7 | 1.23 | 1.054e-06 | 0.013 | 0.556 |
AGE | Mean (SD) | 57.68 (14) |
Significant markers | N = 76 | |
pos. correlated | 42 | |
neg. correlated | 34 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
RANBP17 | -0.316 | 1.677e-13 | 2.02e-09 |
FBXO17 | 0.3024 | 1.966e-12 | 2.37e-08 |
TUSC3 | -0.2972 | 4.787e-12 | 5.76e-08 |
KIAA0495 | 0.279 | 9.796e-11 | 1.18e-06 |
NOL3 | 0.2745 | 2.002e-10 | 2.41e-06 |
PPA1 | -0.2725 | 2.734e-10 | 3.29e-06 |
H2AFY2 | -0.2638 | 1.037e-09 | 1.25e-05 |
DRG2 | 0.2628 | 1.203e-09 | 1.45e-05 |
NCOA4 | -0.2621 | 1.343e-09 | 1.62e-05 |
ENOSF1 | -0.2585 | 2.273e-09 | 2.73e-05 |
GENDER | Labels | N |
FEMALE | 205 | |
MALE | 314 | |
Significant markers | N = 23 | |
Higher in MALE | 11 | |
Higher in FEMALE | 12 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
DDX3Y | 36.83 | 2.924e-138 | 3.52e-134 | 0.9584 |
RPS4Y1 | 39.2 | 2.833e-135 | 3.41e-131 | 0.9492 |
EIF1AY | 34.4 | 1.476e-131 | 1.78e-127 | 0.9528 |
JARID1D | 33.72 | 3.527e-131 | 4.25e-127 | 0.9563 |
NLGN4Y | 30.21 | 1.062e-114 | 1.28e-110 | 0.9458 |
USP9Y | 21.03 | 3.406e-71 | 4.1e-67 | 0.9156 |
CYORF15B | 19.1 | 6.738e-62 | 8.11e-58 | 0.9006 |
UTY | 19.44 | 8.975e-59 | 1.08e-54 | 0.8959 |
ZFX | -12.4 | 1.482e-29 | 1.78e-25 | 0.8181 |
HDHD1A | -12.31 | 2.604e-29 | 3.13e-25 | 0.802 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 77.12 (14) |
Significant markers | N = 0 |
One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 350 | |
YES | 169 | |
Significant markers | N = 1 | |
Higher in YES | 0 | |
Higher in NO | 1 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
NPAT | -5.31 | 1.811e-07 | 0.00218 | 0.6241 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 273 | |
YES | 246 | |
Significant markers | N = 8 | |
Higher in YES | 0 | |
Higher in NO | 8 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
WDR57 | -5.78 | 1.322e-08 | 0.000159 | 0.6419 |
SSNA1 | -5.33 | 1.434e-07 | 0.00173 | 0.6399 |
SMU1 | -5.32 | 1.525e-07 | 0.00184 | 0.6245 |
DNAJA2 | -5.05 | 6.073e-07 | 0.00731 | 0.6297 |
IDH3A | -4.97 | 9.321e-07 | 0.0112 | 0.6245 |
PDCL | -4.88 | 1.425e-06 | 0.0172 | 0.6275 |
NUTF2 | -4.82 | 1.884e-06 | 0.0227 | 0.6112 |
RPN1 | -4.65 | 4.157e-06 | 0.05 | 0.6192 |
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Expresson data file = GBM.medianexp.txt
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Clinical data file = GBM.clin.merged.picked.txt
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Number of patients = 519
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Number of genes = 12042
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Number of clinical features = 6
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.