This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 142 genes and 8 clinical features across 408 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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16 genes correlated to 'AGE'.
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ESR1|ER-ALPHA , STMN1|STATHMIN , CDC2|CDK1 , KIT|C-KIT , MET|C-MET_PY1235 , ...
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1 gene correlated to 'LYMPH.NODE.METASTASIS'.
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ERRFI1|MIG-6
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No genes correlated to 'Time to Death', 'GENDER', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'DISTANT.METASTASIS', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at Q value < 0.05.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=16 | older | N=6 | younger | N=10 |
GENDER | t test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
DISTANT METASTASIS | ANOVA test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=1 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=0 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.1-189 (median=24.5) |
censored | N = 336 | |
death | N = 44 | |
Significant markers | N = 0 |
Table S2. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 57.85 (13) |
Significant markers | N = 16 | |
pos. correlated | 6 | |
neg. correlated | 10 |
Table S3. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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ESR1|ER-ALPHA | 0.3845 | 8.013e-16 | 1.14e-13 |
STMN1|STATHMIN | -0.2322 | 2.125e-06 | 3e-04 |
CDC2|CDK1 | -0.217 | 9.725e-06 | 0.00136 |
KIT|C-KIT | -0.2159 | 1.09e-05 | 0.00151 |
MET|C-MET_PY1235 | -0.2153 | 1.152e-05 | 0.00159 |
AR|AR | 0.2085 | 2.189e-05 | 0.003 |
CDH3|P-CADHERIN | -0.2082 | 2.242e-05 | 0.00305 |
EGFR|EGFR | -0.2067 | 2.582e-05 | 0.00349 |
NOTCH1|NOTCH1 | -0.1931 | 8.668e-05 | 0.0116 |
TSC2|TUBERIN | 0.1914 | 0.0001003 | 0.0133 |
Figure S1. Get High-res Image As an example, this figure shows the association of ESR1|ER-ALPHA to 'AGE'. P value = 8.01e-16 with Spearman correlation analysis. The straight line presents the best linear regression.
![](V2ex.png)
Table S4. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 403 | |
MALE | 5 | |
Significant markers | N = 0 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S5. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 125 | |
YES | 283 | |
Significant markers | N = 0 |
Table S6. Basic characteristics of clinical feature: 'DISTANT.METASTASIS'
DISTANT.METASTASIS | Labels | N |
CM0 (I+) | 1 | |
M0 | 293 | |
M1 | 8 | |
MX | 5 | |
Significant markers | N = 0 |
Table S7. Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 86 | |
N0 (I+) | 7 | |
N0 (I-) | 47 | |
N1 | 36 | |
N1A | 53 | |
N1B | 4 | |
N1C | 1 | |
N1MI | 10 | |
N2 | 20 | |
N2A | 22 | |
N3 | 4 | |
N3A | 13 | |
NX | 4 | |
Significant markers | N = 1 |
Table S8. Get Full Table List of one gene differentially expressed by 'LYMPH.NODE.METASTASIS'
ANOVA_P | Q | |
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ERRFI1|MIG-6 | 0.0002244 | 0.0319 |
Figure S2. Get High-res Image As an example, this figure shows the association of ERRFI1|MIG-6 to 'LYMPH.NODE.METASTASIS'. P value = 0.000224 with ANOVA analysis.
![](V6ex.png)
Table S9. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1.86 (3.5) |
Significant markers | N = 0 |
Table S10. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 30 | |
STAGE IA | 15 | |
STAGE IB | 1 | |
STAGE IIA | 105 | |
STAGE IIB | 74 | |
STAGE IIIA | 49 | |
STAGE IIIB | 10 | |
STAGE IIIC | 10 | |
STAGE IV | 8 | |
STAGE X | 5 | |
Significant markers | N = 0 |
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Expresson data file = BRCA-TP.rppa.txt
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Clinical data file = BRCA-TP.clin.merged.picked.txt
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Number of patients = 408
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Number of genes = 142
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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 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.