This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 174 genes and 9 clinical features across 212 samples, statistically thresholded by Q value < 0.05, 6 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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1 gene correlated to 'GENDER'.
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MAPK14|P38_PT180_Y182-R-V
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2 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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BCL2|BCL-2-R-C , COL6A1|COLLAGEN_VI-R-V
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1 gene correlated to 'NUMBERPACKYEARSSMOKED'.
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CHEK2|CHK2-M-C
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3 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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ANXA1|ANNEXIN_I-R-V , SRC|SRC_PY416-R-C , YAP1|YAP_PS127-R-C
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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MAPK1 MAPK3|MAPK_PT202_Y204-R-V , MAP2K1|MEK1_PS217_S221-R-V
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No genes correlated to 'AGE', 'YEAROFTOBACCOSMOKINGONSET', and 'LYMPH.NODE.METASTASIS'.
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=1 | male | N=0 | female | N=1 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=2 | yes | N=0 | no | N=2 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=1 | higher numberpackyearssmoked | N=1 | lower numberpackyearssmoked | N=0 |
YEAROFTOBACCOSMOKINGONSET | Spearman correlation test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=3 | higher number.of.lymph.nodes | N=0 | lower number.of.lymph.nodes | N=3 |
NEOPLASM DISEASESTAGE | ANOVA test | N=2 |
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 | |
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SMAD3|SMAD3-R-V | 3.5 | 0.0001412 | 0.025 | 0.581 |
AGE | Mean (SD) | 62.12 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 62 | |
MALE | 150 | |
Significant markers | N = 1 | |
Higher in MALE | 0 | |
Higher in FEMALE | 1 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
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MAPK14|P38_PT180_Y182-R-V | -3.86 | 0.0001831 | 0.0319 | 0.6624 |
2 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 58 | |
YES | 154 | |
Significant markers | N = 2 | |
Higher in YES | 0 | |
Higher in NO | 2 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
BCL2|BCL-2-R-C | -4.31 | 4.8e-05 | 0.00835 | 0.7071 |
COL6A1|COLLAGEN_VI-R-V | -3.99 | 0.0001411 | 0.0244 | 0.6773 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 48.65 (38) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
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CHEK2|CHK2-M-C | 0.3495 | 0.0002242 | 0.039 |
YEAROFTOBACCOSMOKINGONSET | Mean (SD) | 1964.27 (12) |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 72 | |
N1 | 21 | |
N2 | 4 | |
N2A | 4 | |
N2B | 45 | |
N2C | 26 | |
N3 | 4 | |
NX | 34 | |
Significant markers | N = 0 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.86 (5.1) |
Significant markers | N = 3 | |
pos. correlated | 0 | |
neg. correlated | 3 |
SpearmanCorr | corrP | Q | |
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ANXA1|ANNEXIN_I-R-V | -0.3328 | 9.218e-06 | 0.0016 |
SRC|SRC_PY416-R-C | -0.2985 | 7.711e-05 | 0.0133 |
YAP1|YAP_PS127-R-C | -0.2805 | 0.0002115 | 0.0364 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 9 | |
STAGE II | 39 | |
STAGE III | 31 | |
STAGE IVA | 117 | |
STAGE IVB | 4 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | 6.74e-05 | 0.0117 |
MAP2K1|MEK1_PS217_S221-R-V | 0.0001008 | 0.0174 |
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Expresson data file = HNSC-TP.rppa.txt
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Clinical data file = HNSC-TP.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 = 9
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 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 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.