This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18585 genes and 5 clinical features across 333 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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1 gene correlated to 'Time to Death'.
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KCNK10|54207
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259 genes correlated to 'AGE'.
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DIO2|1734 , MGAT4A|11320 , TNFAIP2|7127 , HIF3A|64344 , DACT1|51339 , ...
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2047 genes correlated to 'HISTOLOGICAL.TYPE'.
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L1CAM|3897 , KIAA1324|57535 , CLDN6|9074 , SPDEF|25803 , TFF3|7033 , ...
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3 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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F13A1|2162 , COG5|10466 , C8ORF79|57604
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No genes correlated to 'NEOADJUVANT.THERAPY'
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=1 | shorter survival | N=1 | longer survival | N=0 |
AGE | Spearman correlation test | N=259 | older | N=148 | younger | N=111 |
HISTOLOGICAL TYPE | ANOVA test | N=2047 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=3 | yes | N=3 | no | N=0 |
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0-187.1 (median=18.2) |
censored | N = 304 | |
death | N = 28 | |
Significant markers | N = 1 | |
associated with shorter survival | 1 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
KCNK10|54207 | 1.95 | 2.202e-07 | 0.0041 | 0.738 |
AGE | Mean (SD) | 63.23 (11) |
Significant markers | N = 259 | |
pos. correlated | 148 | |
neg. correlated | 111 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
DIO2|1734 | -0.4205 | 1.069e-15 | 1.99e-11 |
MGAT4A|11320 | 0.373 | 1.97e-12 | 3.66e-08 |
TNFAIP2|7127 | 0.3729 | 2.012e-12 | 3.74e-08 |
HIF3A|64344 | 0.3737 | 3.039e-12 | 5.65e-08 |
DACT1|51339 | -0.363 | 8.302e-12 | 1.54e-07 |
FAM107A|11170 | 0.3628 | 8.504e-12 | 1.58e-07 |
NR2F6|2063 | 0.3548 | 2.57e-11 | 4.77e-07 |
GPR158|57512 | 0.3951 | 2.949e-11 | 5.48e-07 |
DUSP9|1852 | 0.3712 | 3.112e-11 | 5.78e-07 |
AEN|64782 | -0.351 | 4.36e-11 | 8.1e-07 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 252 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | 3 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | 7 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | 2 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | 7 | |
MIXED SEROUS AND ENDOMETRIOID | 10 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 52 | |
Significant markers | N = 2047 |
ANOVA_P | Q | |
---|---|---|
L1CAM|3897 | 6.712e-43 | 1.25e-38 |
KIAA1324|57535 | 1.749e-40 | 3.25e-36 |
CLDN6|9074 | 2.003e-33 | 3.72e-29 |
SPDEF|25803 | 4.351e-31 | 8.09e-27 |
TFF3|7033 | 9.558e-31 | 1.78e-26 |
GRB7|2886 | 1.703e-30 | 3.16e-26 |
SLC6A12|6539 | 3.543e-30 | 6.58e-26 |
HIF3A|64344 | 5.31e-28 | 9.87e-24 |
FOXA2|3170 | 4.914e-27 | 9.13e-23 |
SLC6A10P|386757 | 5.379e-27 | 9.99e-23 |
3 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 115 | |
YES | 218 | |
Significant markers | N = 3 | |
Higher in YES | 3 | |
Higher in NO | 0 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
F13A1|2162 | 4.91 | 1.626e-06 | 0.0302 | 0.6587 |
COG5|10466 | 4.89 | 1.816e-06 | 0.0337 | 0.6548 |
C8ORF79|57604 | 4.83 | 2.627e-06 | 0.0488 | 0.6585 |
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Expresson data file = UCEC.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = UCEC.clin.merged.picked.txt
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Number of patients = 333
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Number of genes = 18585
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Number of clinical features = 5
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 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 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 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.