This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18744 genes and 5 clinical features across 266 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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135 genes correlated to 'AGE'.
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DIO2|1734 , DACT1|51339 , TNFAIP2|7127 , S100A1|6271 , CYGB|114757 , ...
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1392 genes correlated to 'HISTOLOGICAL.TYPE'.
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KIAA1324|57535 , L1CAM|3897 , SPDEF|25803 , HIF3A|64344 , CLDN6|9074 , ...
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11 genes correlated to 'NEOADJUVANT.THERAPY'.
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RANGRF|29098 , WFDC1|58189 , ANAPC4|29945 , NPDC1|56654 , IHH|3549 , ...
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No genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'
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=1 | shorter survival | N=1 | longer survival | N=0 |
AGE | Spearman correlation test | N=135 | older | N=51 | younger | N=84 |
HISTOLOGICAL TYPE | ANOVA test | N=1392 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
NEOADJUVANT THERAPY | t test | N=11 | yes | N=10 | no | N=1 |
Time to Death | Duration (Months) | 0-173.6 (median=20.2) |
censored | N = 246 | |
death | N = 20 | |
Significant markers | N = 1 | |
associated with shorter survival | 1 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
KCNK10|54207 | 2.4 | 1.168e-07 | 0.0022 | 0.763 |
AGE | Mean (SD) | 63.13 (11) |
Significant markers | N = 135 | |
pos. correlated | 51 | |
neg. correlated | 84 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
DIO2|1734 | -0.4108 | 2.977e-12 | 5.58e-08 |
DACT1|51339 | -0.3832 | 9.863e-11 | 1.85e-06 |
TNFAIP2|7127 | 0.3737 | 3.044e-10 | 5.7e-06 |
S100A1|6271 | 0.372 | 3.737e-10 | 7e-06 |
CYGB|114757 | -0.362 | 1.172e-09 | 2.2e-05 |
PTCH1|5727 | -0.3515 | 3.729e-09 | 6.99e-05 |
DLC1|10395 | -0.3505 | 4.169e-09 | 7.81e-05 |
KIAA1199|57214 | -0.3491 | 4.877e-09 | 9.14e-05 |
PDGFRB|5159 | -0.3486 | 5.103e-09 | 9.56e-05 |
PHLDA1|22822 | -0.3471 | 6.024e-09 | 0.000113 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 205 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | 3 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | 4 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | 1 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | 5 | |
MIXED SEROUS AND ENDOMETRIOID | 7 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 41 | |
Significant markers | N = 1392 |
ANOVA_P | Q | |
---|---|---|
KIAA1324|57535 | 3.201e-41 | 6e-37 |
L1CAM|3897 | 6.779e-35 | 1.27e-30 |
SPDEF|25803 | 8.597e-33 | 1.61e-28 |
HIF3A|64344 | 9.313e-30 | 1.75e-25 |
CLDN6|9074 | 1.3e-27 | 2.44e-23 |
TFF3|7033 | 2.257e-27 | 4.23e-23 |
SLC6A12|6539 | 5.885e-27 | 1.1e-22 |
FOXA2|3170 | 2.98e-26 | 5.58e-22 |
FIGNL2|401720 | 3.16e-26 | 5.92e-22 |
IL20RA|53832 | 1.441e-25 | 2.7e-21 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 99 | |
YES | 167 | |
Significant markers | N = 0 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 83 | |
YES | 183 | |
Significant markers | N = 11 | |
Higher in YES | 10 | |
Higher in NO | 1 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
RANGRF|29098 | 5.61 | 8.45e-08 | 0.00158 | 0.6981 |
WFDC1|58189 | 5.14 | 8.394e-07 | 0.0157 | 0.6877 |
ANAPC4|29945 | 5.03 | 1.239e-06 | 0.0232 | 0.6803 |
NPDC1|56654 | 5.07 | 1.24e-06 | 0.0232 | 0.7089 |
IHH|3549 | 5.03 | 1.431e-06 | 0.0268 | 0.6894 |
NEIL1|79661 | 5.03 | 1.466e-06 | 0.0275 | 0.6854 |
CEBPB|1051 | -4.99 | 1.764e-06 | 0.0331 | 0.6904 |
KIAA1324|57535 | 4.99 | 1.838e-06 | 0.0344 | 0.6773 |
C19ORF45|374877 | 4.95 | 2.005e-06 | 0.0376 | 0.6815 |
HSF4|3299 | 4.91 | 2.337e-06 | 0.0438 | 0.6865 |
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Expresson data file = UCEC.mRNAseq_RPKM_log2.txt
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Clinical data file = UCEC.clin.merged.picked.txt
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Number of patients = 266
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Number of genes = 18744
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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.