This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 189 genes and 8 clinical features across 258 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one genes.
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31 genes correlated to 'Time to Death'.
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ANXA1|ANNEXIN-1-M-E , PGR|PR-R-V , MAPK14|P38_MAPK-R-V , BAX|BAX-R-V , SERPINE1|PAI-1-M-E , ...
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7 genes correlated to 'AGE'.
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PEA15|PEA15-R-V , IGFBP2|IGFBP2-R-V , SERPINE1|PAI-1-M-E , EGFR|EGFR-R-V , ANXA1|ANNEXIN-1-M-E , ...
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3 genes correlated to 'GENDER'.
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STAT5A|STAT5-ALPHA-R-V , RAB11A RAB11B|RAB11-R-E , TSC1|TSC1-R-C
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1 gene correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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IGFBP2|IGFBP2-R-V
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43 genes correlated to 'HISTOLOGICAL.TYPE'.
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SYK|SYK-M-V , ANXA1|ANNEXIN-1-M-E , AR|AR-R-V , YAP1|YAP_PS127-R-E , BAX|BAX-R-V , ...
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No genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION', 'RACE', and 'ETHNICITY'.
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=31 | shorter survival | N=14 | longer survival | N=17 |
AGE | Spearman correlation test | N=7 | older | N=6 | younger | N=1 |
GENDER | Wilcoxon test | N=3 | male | N=3 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=1 | higher score | N=0 | lower score | N=1 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=43 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
RACE | Wilcoxon test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0-211.2 (median=17.1) |
censored | N = 199 | |
death | N = 57 | |
Significant markers | N = 31 | |
associated with shorter survival | 14 | |
associated with longer survival | 17 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
ANXA1|ANNEXIN-1-M-E | 2.2 | 1.464e-08 | 2.8e-06 | 0.737 |
PGR|PR-R-V | 0 | 8.471e-06 | 0.0016 | 0.293 |
MAPK14|P38_MAPK-R-V | 3.7 | 1.172e-05 | 0.0022 | 0.693 |
BAX|BAX-R-V | 5.6 | 2.859e-05 | 0.0053 | 0.688 |
SERPINE1|PAI-1-M-E | 2.2 | 2.948e-05 | 0.0055 | 0.684 |
INPP4B|INPP4B-G-E | 0.12 | 3.353e-05 | 0.0062 | 0.34 |
IGFBP2|IGFBP2-R-V | 2.1 | 3.715e-05 | 0.0068 | 0.748 |
CHEK2|CHK2_PT68-R-E | 0.03 | 6.536e-05 | 0.012 | 0.315 |
SMAD1|SMAD1-R-V | 5.2 | 7.34e-05 | 0.013 | 0.651 |
SCD1|SCD1-M-V | 0.04 | 7.524e-05 | 0.014 | 0.276 |
AGE | Mean (SD) | 42.4 (13) |
Significant markers | N = 7 | |
pos. correlated | 6 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
PEA15|PEA15-R-V | -0.2972 | 1.171e-06 | 0.000221 |
IGFBP2|IGFBP2-R-V | 0.2915 | 1.908e-06 | 0.000359 |
SERPINE1|PAI-1-M-E | 0.2596 | 2.417e-05 | 0.00452 |
EGFR|EGFR-R-V | 0.2152 | 0.0004989 | 0.0928 |
ANXA1|ANNEXIN-1-M-E | 0.205 | 0.0009271 | 0.172 |
ASNS|ASNS-R-V | 0.2049 | 0.0009342 | 0.172 |
CDKN1A|P21-R-V | 0.1954 | 0.001609 | 0.294 |
GENDER | Labels | N |
FEMALE | 111 | |
MALE | 147 | |
Significant markers | N = 3 | |
Higher in MALE | 3 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
STAT5A|STAT5-ALPHA-R-V | 5918 | 0.0001603 | 0.0303 | 0.6373 |
RAB11A RAB11B|RAB11-R-E | 10306.5 | 0.0002961 | 0.0557 | 0.6316 |
TSC1|TSC1-R-C | 6238 | 0.001215 | 0.227 | 0.6177 |
One gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 86.7 (12) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
IGFBP2|IGFBP2-R-V | -0.3532 | 0.0001078 | 0.0204 |
HISTOLOGICAL.TYPE | Labels | N |
ASTROCYTOMA | 86 | |
OLIGOASTROCYTOMA | 70 | |
OLIGODENDROGLIOMA | 102 | |
Significant markers | N = 43 |
ANOVA_P | Q | |
---|---|---|
SYK|SYK-M-V | 3.132e-15 | 5.92e-13 |
ANXA1|ANNEXIN-1-M-E | 2.39e-10 | 4.49e-08 |
AR|AR-R-V | 3.808e-08 | 7.12e-06 |
YAP1|YAP_PS127-R-E | 6.511e-08 | 1.21e-05 |
BAX|BAX-R-V | 9.291e-08 | 1.72e-05 |
ERBB3|HER3_PY1289-R-C | 3.14e-07 | 5.78e-05 |
MAPK14|P38_MAPK-R-V | 4.57e-07 | 8.36e-05 |
KIT|C-KIT-R-V | 1.549e-06 | 0.000282 |
BAD|BAD_PS112-R-V | 1.832e-06 | 0.000332 |
STAT3|STAT3_PY705-R-V | 7.607e-06 | 0.00137 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 84 | |
YES | 174 | |
Significant markers | N = 0 |
RACE | Labels | N |
BLACK OR AFRICAN AMERICAN | 11 | |
WHITE | 246 | |
Significant markers | N = 0 |
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Expresson data file = LGG-TP.rppa.txt
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Clinical data file = LGG-TP.merged_data.txt
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Number of patients = 258
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Number of genes = 189
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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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.