This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 5 clinical features across 54 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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144 genes correlated to 'HISTOLOGICAL.TYPE'.
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KLHL34 , OR4S2 , C19ORF12 , TSP50 , KIAA1324 , ...
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29 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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RHOXF1 , GALNTL5 , AGTR1 , LBP , ANKS1A , ...
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No genes correlated to 'Time to Death', 'AGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at Q value < 0.05.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=144 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
COMPLETENESS OF RESECTION | ANOVA test | N=29 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 6-133.2 (median=35.4) |
censored | N = 47 | |
death | N = 7 | |
Significant markers | N = 0 |
Table S2. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 62.94 (12) |
Significant markers | N = 0 |
Table S3. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 41 | |
MIXED SEROUS AND ENDOMETRIOID | 1 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 12 | |
Significant markers | N = 144 |
Table S4. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'
ANOVA_P | Q | |
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KLHL34 | 8.095e-17 | 1.44e-12 |
OR4S2 | 1.38e-14 | 2.46e-10 |
C19ORF12 | 3.022e-14 | 5.38e-10 |
TSP50 | 2.904e-13 | 5.17e-09 |
KIAA1324 | 2.954e-13 | 5.26e-09 |
PNOC | 9.543e-13 | 1.7e-08 |
FOXA2 | 1.393e-12 | 2.48e-08 |
CDH6 | 2.506e-12 | 4.46e-08 |
CLDN6 | 2.018e-11 | 3.59e-07 |
ANXA10 | 8.888e-11 | 1.58e-06 |
Figure S1. Get High-res Image As an example, this figure shows the association of KLHL34 to 'HISTOLOGICAL.TYPE'. P value = 8.1e-17 with ANOVA analysis.
![](V3ex.png)
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S5. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 25 | |
YES | 29 | |
Significant markers | N = 0 |
Table S6. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 39 | |
R1 | 6 | |
R2 | 2 | |
RX | 1 | |
Significant markers | N = 29 |
Table S7. Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'
ANOVA_P | Q | |
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RHOXF1 | 1.352e-13 | 2.41e-09 |
GALNTL5 | 3.481e-10 | 6.2e-06 |
AGTR1 | 9.628e-10 | 1.71e-05 |
LBP | 1.947e-09 | 3.47e-05 |
ANKS1A | 6.188e-09 | 0.00011 |
C12ORF59 | 8.975e-09 | 0.00016 |
ABHD9 | 2.991e-08 | 0.000533 |
LANCL2 | 3.861e-08 | 0.000688 |
SSX7 | 4.419e-08 | 0.000787 |
KCNV1 | 4.506e-08 | 0.000802 |
Figure S2. Get High-res Image As an example, this figure shows the association of RHOXF1 to 'COMPLETENESS.OF.RESECTION'. P value = 1.35e-13 with ANOVA analysis.
![](V5ex.png)
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Expresson data file = UCEC-TP.medianexp.txt
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Clinical data file = UCEC-TP.clin.merged.picked.txt
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Number of patients = 54
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Number of genes = 17814
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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.