This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 142 genes and 9 clinical features across 408 samples, statistically thresholded by Q value < 0.05, 5 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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6 genes correlated to 'HISTOLOGICAL.TYPE'.
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CDH1|E-CADHERIN , CTNNB1|BETA-CATENIN , CTNNA1|ALPHA-CATENIN , TP53|P53 , CLDN7|CLAUDIN-7 , ...
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1 gene correlated to 'DISTANT.METASTASIS'.
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BCL2L1|BCL-XL
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4 genes correlated to 'LYMPH.NODE.METASTASIS'.
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PIK3CA |PI3K-P110-ALPHA , ERRFI1|MIG-6 , NF2|NF2 , EIF4EBP1|4E-BP1_PS65
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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BCL2L1|BCL-XL , COL6A1|COLLAGEN_VI
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No genes correlated to 'Time to Death', 'GENDER', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NUMBER.OF.LYMPH.NODES'.
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=0 | ||||
AGE | Spearman correlation test | N=16 | older | N=6 | younger | N=10 |
GENDER | t test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=6 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
DISTANT METASTASIS | ANOVA test | N=1 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=4 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=2 |
Time to Death | Duration (Months) | 0.1-189 (median=24.5) |
censored | N = 336 | |
death | N = 44 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 57.85 (13) |
Significant markers | N = 16 | |
pos. correlated | 6 | |
neg. correlated | 10 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
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 |
GENDER | Labels | N |
FEMALE | 403 | |
MALE | 5 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
INFILTRATING DUCTAL CARCINOMA | 353 | |
INFILTRATING LOBULAR CARCINOMA | 30 | |
MEDULLARY CARCINOMA | 1 | |
MIXED HISTOLOGY (PLEASE SPECIFY) | 7 | |
MUCINOUS CARCINOMA | 2 | |
OTHER SPECIFY | 15 | |
Significant markers | N = 6 |
ANOVA_P | Q | |
---|---|---|
CDH1|E-CADHERIN | 1.776e-37 | 2.52e-35 |
CTNNB1|BETA-CATENIN | 1.443e-18 | 2.04e-16 |
CTNNA1|ALPHA-CATENIN | 8.194e-15 | 1.15e-12 |
TP53|P53 | 0.0001428 | 0.0199 |
CLDN7|CLAUDIN-7 | 0.0001921 | 0.0265 |
COL6A1|COLLAGEN_VI | 0.0002369 | 0.0325 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 125 | |
YES | 283 | |
Significant markers | N = 0 |
DISTANT.METASTASIS | Labels | N |
CM0 (I+) | 1 | |
M0 | 386 | |
M1 | 14 | |
MX | 7 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
BCL2L1|BCL-XL | 0.0002307 | 0.0328 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 100 | |
N0 (I+) | 13 | |
N0 (I-) | 79 | |
N1 | 48 | |
N1A | 63 | |
N1B | 8 | |
N1C | 1 | |
N1MI | 12 | |
N2 | 27 | |
N2A | 25 | |
N3 | 9 | |
N3A | 15 | |
N3C | 1 | |
NX | 7 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
PIK3CA |PI3K-P110-ALPHA | 4.101e-28 | 5.82e-26 |
ERRFI1|MIG-6 | 6.684e-06 | 0.000942 |
NF2|NF2 | 8.796e-05 | 0.0123 |
EIF4EBP1|4E-BP1_PS65 | 0.0002749 | 0.0382 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1.86 (3.5) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 30 | |
STAGE IA | 31 | |
STAGE IB | 4 | |
STAGE IIA | 137 | |
STAGE IIB | 94 | |
STAGE IIIA | 62 | |
STAGE IIIB | 13 | |
STAGE IIIC | 15 | |
STAGE IV | 14 | |
STAGE X | 8 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
BCL2L1|BCL-XL | 1.663e-05 | 0.00236 |
COL6A1|COLLAGEN_VI | 0.0001192 | 0.0168 |
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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 = 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.