This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 6 clinical features across 27 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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13 genes correlated to 'GENDER'.
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RPS4Y1 , DDX3Y , RPS4Y2 , EIF1AY , UTY , ...
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1 gene correlated to 'HISTOLOGICAL.TYPE'.
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PCDHA5
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No genes correlated to 'Time to Death', 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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=0 | ||||
GENDER | t test | N=13 | male | N=13 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=1 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 |
Time to Death | Duration (Months) | 0.1-134.3 (median=46.6) |
censored | N = 17 | |
death | N = 10 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 39.33 (9.1) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 9 | |
MALE | 18 | |
Significant markers | N = 13 | |
Higher in MALE | 13 | |
Higher in FEMALE | 0 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
RPS4Y1 | 26.3 | 1.893e-18 | 3.37e-14 | 1 |
DDX3Y | 28 | 2.184e-18 | 3.89e-14 | 1 |
RPS4Y2 | 22.93 | 1.562e-17 | 2.78e-13 | 1 |
EIF1AY | 21.54 | 4.473e-16 | 7.97e-12 | 1 |
UTY | 16.69 | 4.595e-15 | 8.18e-11 | 1 |
TTTY14 | 15.58 | 1.829e-13 | 3.26e-09 | 1 |
JARID1D | 14.28 | 3.923e-12 | 6.99e-08 | 1 |
CYORF15B | 12.12 | 5.86e-12 | 1.04e-07 | 0.9815 |
ZFY | 12.21 | 7.306e-12 | 1.3e-07 | 0.9691 |
NLGN4Y | 9.24 | 1.045e-08 | 0.000186 | 0.963 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 88.82 (12) |
Score | N | |
50 | 1 | |
80 | 3 | |
90 | 8 | |
100 | 5 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ASTROCYTOMA | 10 | |
OLIGOASTROCYTOMA | 9 | |
OLIGODENDROGLIOMA | 8 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
PCDHA5 | 7.453e-09 | 0.000133 |
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Expresson data file = LGG-TP.medianexp.txt
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Clinical data file = LGG-TP.merged_data.txt
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Number of patients = 27
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Number of genes = 17814
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Number of clinical features = 6
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.