(primary solid tumor cohort)
This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 166 genes and 8 clinical features across 454 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.
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38 genes correlated to 'Time to Death'.
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VASP|VASP-R-C , SRC|SRC_PY527-R-V , CDKN1A|P21-R-C , GAB2|GAB2-R-V , ACACA|ACC1-R-C , ...
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1 gene correlated to 'AGE'.
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IGFBP2|IGFBP2-R-V
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4 genes correlated to 'GENDER'.
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AR|AR-R-V , SRC|SRC-M-V , PTK2|FAK-R-C , CLDN7|CLAUDIN-7-R-V
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36 genes correlated to 'PATHOLOGY.T'.
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ERBB3|HER3_PY1298-R-C , CDH3|P-CADHERIN-R-C , SRC|SRC_PY527-R-V , EEF2|EEF2-R-V , ACACA|ACC1-R-C , ...
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1 gene correlated to 'PATHOLOGY.N'.
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EGFR|EGFR_PY1068-R-V
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23 genes correlated to 'PATHOLOGICSPREAD(M)'.
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ERBB3|HER3_PY1298-R-C , PECAM1|CD31-M-V , YBX1|YB-1-R-V , MAPK1 MAPK3|MAPK_PT202_Y204-R-V , TP53BP1|53BP1-R-C , ...
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42 genes correlated to 'TUMOR.STAGE'.
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ERBB3|HER3_PY1298-R-C , CDH3|P-CADHERIN-R-C , SRC|SRC_PY527-R-V , SHC1|SHC_PY317-R-NA , PECAM1|CD31-M-V , ...
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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=38 | shorter survival | N=18 | longer survival | N=20 |
AGE | Spearman correlation test | N=1 | older | N=1 | younger | N=0 |
GENDER | t test | N=4 | male | N=2 | female | N=2 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=36 | higher pT | N=17 | lower pT | N=19 |
PATHOLOGY N | t test | N=1 | n1 | N=0 | n0 | N=1 |
PATHOLOGICSPREAD(M) | t test | N=23 | m1 | N=8 | m0 | N=15 |
TUMOR STAGE | Spearman correlation test | N=42 | higher stage | N=19 | lower stage | N=23 |
Time to Death | Duration (Months) | 0.1-111 (median=34.3) |
censored | N = 301 | |
death | N = 150 | |
Significant markers | N = 38 | |
associated with shorter survival | 18 | |
associated with longer survival | 20 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
VASP|VASP-R-C | 4.3 | 2.018e-11 | 3.3e-09 | 0.637 |
SRC|SRC_PY527-R-V | 0.54 | 3.171e-11 | 5.2e-09 | 0.37 |
CDKN1A|P21-R-C | 6.4 | 4.922e-11 | 8.1e-09 | 0.631 |
GAB2|GAB2-R-V | 0.5 | 8.237e-10 | 1.3e-07 | 0.354 |
ACACA|ACC1-R-C | 2.6 | 1.397e-09 | 2.3e-07 | 0.626 |
CTNNA1|ALPHA-CATENIN-M-V | 0.2 | 1.707e-09 | 2.7e-07 | 0.352 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | 0.61 | 2.621e-09 | 4.2e-07 | 0.349 |
RAD51|RAD51-M-C | 4.1 | 2.664e-09 | 4.2e-07 | 0.633 |
AR|AR-R-V | 0.32 | 4.642e-09 | 7.3e-07 | 0.346 |
PRKAA1|AMPK_PT172-R-V | 0.47 | 5.98e-09 | 9.4e-07 | 0.376 |
AGE | Mean (SD) | 60.42 (12) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
IGFBP2|IGFBP2-R-V | 0.2273 | 1.014e-06 | 0.000168 |
GENDER | Labels | N |
FEMALE | 151 | |
MALE | 303 | |
Significant markers | N = 4 | |
Higher in MALE | 2 | |
Higher in FEMALE | 2 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
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AR|AR-R-V | 4.57 | 6.794e-06 | 0.00113 | 0.6251 |
SRC|SRC-M-V | -3.84 | 0.0001525 | 0.0252 | 0.6096 |
PTK2|FAK-R-C | -3.78 | 0.0001971 | 0.0323 | 0.6063 |
CLDN7|CLAUDIN-7-R-V | 3.74 | 0.0002208 | 0.036 | 0.6239 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 93.53 (7.7) |
Score | N | |
70 | 1 | |
80 | 3 | |
90 | 13 | |
100 | 17 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 1.92 (0.97) |
N | ||
T1 | 224 | |
T2 | 54 | |
T3 | 165 | |
T4 | 11 | |
Significant markers | N = 36 | |
pos. correlated | 17 | |
neg. correlated | 19 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ERBB3|HER3_PY1298-R-C | -0.3199 | 2.924e-12 | 4.85e-10 |
CDH3|P-CADHERIN-R-C | 0.3122 | 1.007e-11 | 1.66e-09 |
SRC|SRC_PY527-R-V | -0.29 | 3.005e-10 | 4.93e-08 |
EEF2|EEF2-R-V | 0.2873 | 4.478e-10 | 7.3e-08 |
ACACA|ACC1-R-C | 0.276 | 2.209e-09 | 3.58e-07 |
SHC1|SHC_PY317-R-NA | -0.2717 | 4.011e-09 | 6.46e-07 |
CTNNA1|ALPHA-CATENIN-M-V | -0.2703 | 4.814e-09 | 7.7e-07 |
PECAM1|CD31-M-V | -0.2677 | 6.88e-09 | 1.09e-06 |
ACACA ACACB|ACC_PS79-R-V | 0.2667 | 7.847e-09 | 1.24e-06 |
YBX1|YB-1_PS102-R-V | 0.2618 | 1.497e-08 | 2.35e-06 |
PATHOLOGY.N | Labels | N |
N0 | 208 | |
N1 | 16 | |
Significant markers | N = 1 | |
Higher in N1 | 0 | |
Higher in N0 | 1 |
T(pos if higher in 'N1') | ttestP | Q | AUC | |
---|---|---|---|---|
EGFR|EGFR_PY1068-R-V | -5.09 | 5.522e-05 | 0.00917 | 0.7713 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 380 | |
M1 | 74 | |
Significant markers | N = 23 | |
Higher in M1 | 8 | |
Higher in M0 | 15 |
T(pos if higher in 'M1') | ttestP | Q | AUC | |
---|---|---|---|---|
ERBB3|HER3_PY1298-R-C | -7.13 | 3.866e-11 | 6.42e-09 | 0.7025 |
PECAM1|CD31-M-V | -5.32 | 4.663e-07 | 7.69e-05 | 0.6658 |
YBX1|YB-1-R-V | 5.04 | 1.591e-06 | 0.000261 | 0.6618 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | -5.04 | 1.935e-06 | 0.000315 | 0.6656 |
TP53BP1|53BP1-R-C | 4.73 | 6.443e-06 | 0.00104 | 0.6734 |
PIK3R1|PI3K-P85-R-V | 4.72 | 7.989e-06 | 0.00129 | 0.6766 |
ERRFI1|MIG-6-M-V | -4.62 | 9.093e-06 | 0.00145 | 0.6369 |
PEA15|PEA-15-R-V | 4.63 | 1.046e-05 | 0.00166 | 0.6642 |
AKT1 AKT2 AKT3|AKT_PS473-R-V | -4.39 | 2.42e-05 | 0.00382 | 0.6352 |
EEF2|EEF2-R-V | 4.4 | 2.65e-05 | 0.00416 | 0.6615 |
TUMOR.STAGE | Mean (SD) | 2.11 (1.2) |
N | ||
Stage 1 | 219 | |
Stage 2 | 43 | |
Stage 3 | 114 | |
Stage 4 | 78 | |
Significant markers | N = 42 | |
pos. correlated | 19 | |
neg. correlated | 23 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ERBB3|HER3_PY1298-R-C | -0.3545 | 6.916e-15 | 1.15e-12 |
CDH3|P-CADHERIN-R-C | 0.3324 | 3.591e-13 | 5.92e-11 |
SRC|SRC_PY527-R-V | -0.3104 | 1.343e-11 | 2.2e-09 |
SHC1|SHC_PY317-R-NA | -0.3068 | 2.381e-11 | 3.88e-09 |
PECAM1|CD31-M-V | -0.2965 | 1.149e-10 | 1.86e-08 |
CTNNA1|ALPHA-CATENIN-M-V | -0.2914 | 2.467e-10 | 3.97e-08 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | -0.2831 | 8.191e-10 | 1.31e-07 |
EEF2|EEF2-R-V | 0.2819 | 9.758e-10 | 1.55e-07 |
RAF1|C-RAF_PS338-R-C | -0.274 | 2.922e-09 | 4.62e-07 |
ACACA ACACB|ACC_PS79-R-V | 0.2715 | 4.12e-09 | 6.47e-07 |
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Expresson data file = KIRC-TP.rppa.txt
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Clinical data file = KIRC-TP.clin.merged.picked.txt
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Number of patients = 454
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Number of genes = 166
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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 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.