This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 174 genes and 8 clinical features across 212 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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1 gene correlated to 'Time to Death'.
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SMAD3|SMAD3-R-V
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2 genes correlated to 'GENDER'.
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MAPK14|P38_PT180_Y182-R-V , PTGS2|COX-2-R-C
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6 genes correlated to 'PATHOLOGY.T'.
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MAPK1 MAPK3|MAPK_PT202_Y204-R-V , RPS6|S6_PS235_S236-R-V , AKT1 AKT2 AKT3|AKT_PS473-R-V , MAPK14|P38_PT180_Y182-R-V , SRC|SRC_PY527-R-V , ...
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3 genes correlated to 'PATHOLOGY.N'.
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SRC|SRC_PY416-R-C , ANXA1|ANNEXIN_I-R-V , YAP1|YAP_PS127-R-C
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3 genes correlated to 'TUMOR.STAGE'.
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MAPK1 MAPK3|MAPK_PT202_Y204-R-V , RPS6|S6_PS235_S236-R-V , ARID1A|ARID1A-M-V
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No genes correlated to 'AGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 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=1 | shorter survival | N=1 | longer survival | N=0 |
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=2 | male | N=1 | female | N=1 |
PATHOLOGY T | Spearman correlation test | N=6 | higher pT | N=1 | lower pT | N=5 |
PATHOLOGY N | Spearman correlation test | N=3 | higher pN | N=0 | lower pN | N=3 |
TUMOR STAGE | Spearman correlation test | N=3 | higher stage | N=1 | lower stage | N=2 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0.1-210.9 (median=13.2) |
censored | N = 105 | |
death | N = 107 | |
Significant markers | N = 1 | |
associated with shorter survival | 1 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
SMAD3|SMAD3-R-V | 3.5 | 0.0001519 | 0.026 | 0.581 |
AGE | Mean (SD) | 62.12 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 62 | |
MALE | 150 | |
Significant markers | N = 2 | |
Higher in MALE | 1 | |
Higher in FEMALE | 1 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
MAPK14|P38_PT180_Y182-R-V | -3.89 | 0.0001658 | 0.0289 | 0.6641 |
PTGS2|COX-2-R-C | 3.85 | 0.0001671 | 0.0289 | 0.6258 |
PATHOLOGY.T | Mean (SD) | 2.97 (0.97) |
N | ||
T1 | 13 | |
T2 | 59 | |
T3 | 53 | |
T4 | 79 | |
Significant markers | N = 6 | |
pos. correlated | 1 | |
neg. correlated | 5 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | -0.3357 | 9.18e-07 | 0.00016 |
RPS6|S6_PS235_S236-R-V | -0.3082 | 7.28e-06 | 0.00126 |
AKT1 AKT2 AKT3|AKT_PS473-R-V | -0.2946 | 1.895e-05 | 0.00326 |
MAPK14|P38_PT180_Y182-R-V | -0.2753 | 6.742e-05 | 0.0115 |
SRC|SRC_PY527-R-V | -0.2737 | 7.472e-05 | 0.0127 |
ARID1A|ARID1A-M-V | 0.2583 | 0.0001914 | 0.0324 |
PATHOLOGY.N | Mean (SD) | 1.08 (0.98) |
N | ||
N0 | 73 | |
N1 | 20 | |
N2 | 79 | |
N3 | 4 | |
Significant markers | N = 3 | |
pos. correlated | 0 | |
neg. correlated | 3 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SRC|SRC_PY416-R-C | -0.3346 | 5.657e-06 | 0.000984 |
ANXA1|ANNEXIN_I-R-V | -0.333 | 6.325e-06 | 0.00109 |
YAP1|YAP_PS127-R-C | -0.2977 | 5.998e-05 | 0.0103 |
TUMOR.STAGE | Mean (SD) | 3.32 (0.94) |
N | ||
Stage 1 | 9 | |
Stage 2 | 39 | |
Stage 3 | 31 | |
Stage 4 | 121 | |
Significant markers | N = 3 | |
pos. correlated | 1 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | -0.279 | 6.297e-05 | 0.011 |
RPS6|S6_PS235_S236-R-V | -0.2744 | 8.411e-05 | 0.0146 |
ARID1A|ARID1A-M-V | 0.2711 | 0.0001032 | 0.0177 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 56 | |
YES | 156 | |
Significant markers | N = 0 |
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Expresson data file = HNSC.rppa.txt
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Clinical data file = HNSC.clin.merged.picked.txt
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Number of patients = 212
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Number of genes = 174
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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.