(All_Samples cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18094 genes and 8 clinical features across 198 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.
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9 genes correlated to 'Time to Death'.
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RAB8B|51762 , PPP3CB|5532 , TLR1|7096 , ARPC5|10092 , AGTPBP1|23287 , ...
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5 genes correlated to 'AGE'.
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ACOX2|8309 , PHKA1|5255 , MCHR1|2847 , CD200|4345 , PTGIS|5740
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282 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
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KRT17|3872 , C7|730 , TP53AIP1|63970 , S100A7|6278 , S100A2|6273 , ...
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20 genes correlated to 'GENDER'.
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ZFY|7544 , CYORF15B|84663 , PRKY|5616 , RPS4Y1|6192 , DDX3Y|8653 , ...
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89 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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KDM4C|23081 , ZFP90|146198 , AQP5|362 , LPP|4026 , EIF4G2|1982 , ...
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4 genes correlated to 'DISTANT.METASTASIS'.
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CLDN6|9074 , CXADRP3|440224 , PRPS1|5631 , LRRC28|123355
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5 genes correlated to 'LYMPH.NODE.METASTASIS'.
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IHH|3549 , NPAS4|266743 , MUC6|4588 , NXNL2|158046 , AMY1A|276
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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TNFSF11|8600 , SLC34A2|10568
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=9 | shorter survival | N=0 | longer survival | N=9 |
AGE | Spearman correlation test | N=5 | older | N=0 | younger | N=5 |
PRIMARY SITE OF DISEASE | ANOVA test | N=282 | ||||
GENDER | t test | N=20 | male | N=14 | female | N=6 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=89 | yes | N=51 | no | N=38 |
DISTANT METASTASIS | ANOVA test | N=4 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=5 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=2 |
Time to Death | Duration (Months) | 0.1-98.8 (median=10.5) |
censored | N = 56 | |
death | N = 54 | |
Significant markers | N = 9 | |
associated with shorter survival | 0 | |
associated with longer survival | 9 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
RAB8B|51762 | 0.41 | 1.721e-07 | 0.0031 | 0.33 |
PPP3CB|5532 | 0.31 | 3.549e-07 | 0.0064 | 0.337 |
TLR1|7096 | 0.6 | 4.243e-07 | 0.0077 | 0.301 |
ARPC5|10092 | 0.27 | 6.626e-07 | 0.012 | 0.315 |
AGTPBP1|23287 | 0.48 | 8.418e-07 | 0.015 | 0.333 |
CYB5R4|51167 | 0.59 | 8.846e-07 | 0.016 | 0.327 |
LMBRD1|55788 | 0.41 | 1.307e-06 | 0.024 | 0.309 |
IBTK|25998 | 0.56 | 1.75e-06 | 0.032 | 0.332 |
CUL2|8453 | 0.5 | 2.447e-06 | 0.044 | 0.351 |
AGE | Mean (SD) | 56.64 (16) |
Significant markers | N = 5 | |
pos. correlated | 0 | |
neg. correlated | 5 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ACOX2|8309 | -0.4008 | 6.967e-09 | 0.000126 |
PHKA1|5255 | -0.3887 | 2.143e-08 | 0.000388 |
MCHR1|2847 | -0.3532 | 4.7e-07 | 0.0085 |
CD200|4345 | -0.341 | 1.141e-06 | 0.0206 |
PTGIS|5740 | -0.3334 | 2.038e-06 | 0.0369 |
PRIMARY.SITE.OF.DISEASE | Labels | N |
DISTANT METASTASIS | 27 | |
PRIMARY TUMOR | 24 | |
REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | 35 | |
REGIONAL LYMPH NODE | 112 | |
Significant markers | N = 282 |
ANOVA_P | Q | |
---|---|---|
KRT17|3872 | 1.384e-16 | 2.5e-12 |
C7|730 | 3.95e-15 | 7.15e-11 |
TP53AIP1|63970 | 1.818e-13 | 3.29e-09 |
S100A7|6278 | 2.279e-13 | 4.12e-09 |
S100A2|6273 | 2.662e-13 | 4.82e-09 |
PLA2G4F|255189 | 3.899e-13 | 7.05e-09 |
SPRR1B|6699 | 4.954e-13 | 8.96e-09 |
SERPINB4|6318 | 8.095e-13 | 1.46e-08 |
FLG2|388698 | 8.443e-13 | 1.53e-08 |
KRT10|3858 | 8.65e-13 | 1.56e-08 |
GENDER | Labels | N |
FEMALE | 75 | |
MALE | 123 | |
Significant markers | N = 20 | |
Higher in MALE | 14 | |
Higher in FEMALE | 6 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
ZFY|7544 | 32.67 | 6.143e-76 | 1.11e-71 | 0.9928 |
CYORF15B|84663 | 34.4 | 3.32e-65 | 6e-61 | 1 |
PRKY|5616 | 29 | 1.119e-63 | 2.02e-59 | 0.9951 |
RPS4Y1|6192 | 31.59 | 7.482e-50 | 1.35e-45 | 1 |
DDX3Y|8653 | 33.69 | 1.469e-49 | 2.66e-45 | 0.9982 |
XIST|7503 | -20.9 | 1.219e-48 | 2.21e-44 | 0.9703 |
KDM5D|8284 | 31.86 | 4.122e-44 | 7.45e-40 | 0.9938 |
EIF1AY|9086 | 30.83 | 1.016e-36 | 1.84e-32 | 0.9959 |
TSIX|9383 | -15.94 | 8.088e-34 | 1.46e-29 | 0.9642 |
USP9Y|8287 | 28.09 | 7.241e-33 | 1.31e-28 | 0.9993 |
89 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 3 | |
YES | 195 | |
Significant markers | N = 89 | |
Higher in YES | 51 | |
Higher in NO | 38 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
KDM4C|23081 | -26.05 | 1.821e-46 | 2.95e-42 | 0.9846 |
ZFP90|146198 | -13.86 | 1.316e-30 | 2.13e-26 | 0.8906 |
AQP5|362 | 15.48 | 5.885e-30 | 9.54e-26 | 0.9337 |
LPP|4026 | -12.98 | 1.001e-26 | 1.62e-22 | 0.8393 |
EIF4G2|1982 | -11.71 | 1.077e-22 | 1.75e-18 | 0.8598 |
TBC1D5|9779 | -14.26 | 2.329e-22 | 3.77e-18 | 0.8957 |
HIST3H2A|92815 | 14.48 | 3.902e-21 | 6.32e-17 | 0.875 |
PSCA|8000 | 11.59 | 5.265e-21 | 8.53e-17 | 0.8048 |
GPI|2821 | 11.05 | 1.002e-20 | 1.62e-16 | 0.8137 |
DMRTA2|63950 | 11.41 | 2.895e-19 | 4.69e-15 | 0.8847 |
DISTANT.METASTASIS | Labels | N |
M0 | 172 | |
M1 | 2 | |
M1A | 2 | |
M1B | 2 | |
M1C | 3 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
CLDN6|9074 | 2.626e-09 | 4.75e-05 |
CXADRP3|440224 | 1.071e-07 | 0.00194 |
PRPS1|5631 | 6.116e-07 | 0.0111 |
LRRC28|123355 | 1.57e-06 | 0.0284 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 109 | |
N1 | 2 | |
N1A | 7 | |
N1B | 17 | |
N2 | 1 | |
N2A | 5 | |
N2B | 13 | |
N2C | 6 | |
N3 | 18 | |
NX | 5 | |
Significant markers | N = 5 |
ANOVA_P | Q | |
---|---|---|
IHH|3549 | 8.61e-13 | 1.56e-08 |
NPAS4|266743 | 3.038e-08 | 0.00055 |
MUC6|4588 | 1.803e-07 | 0.00326 |
NXNL2|158046 | 7.127e-07 | 0.0129 |
AMY1A|276 | 1.49e-06 | 0.027 |
NEOPLASM.DISEASESTAGE | Labels | N |
I OR II NOS | 4 | |
STAGE I | 17 | |
STAGE IA | 10 | |
STAGE IB | 15 | |
STAGE II | 20 | |
STAGE IIA | 9 | |
STAGE IIB | 10 | |
STAGE IIC | 22 | |
STAGE III | 9 | |
STAGE IIIA | 6 | |
STAGE IIIB | 20 | |
STAGE IIIC | 26 | |
STAGE IV | 7 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
TNFSF11|8600 | 2.946e-08 | 0.000533 |
SLC34A2|10568 | 6.71e-07 | 0.0121 |
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Expresson data file = SKCM-All_Samples.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = SKCM-All_Samples.clin.merged.picked.txt
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Number of patients = 198
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Number of genes = 18094
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Number of clinical features = 8
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 multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' 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.