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, 3 clinical features related to at least one genes.
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3 genes correlated to 'AGE'.
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NPTX1 , TMEM79 , IL20RB
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150 genes correlated to 'HISTOLOGICAL.TYPE'.
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KLHL34 , OR4S2 , C19ORF12 , TSP50 , KIAA1324 , ...
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28 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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RHOXF1 , GALNTL5 , AGTR1 , LBP , ABHD9 , ...
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No genes correlated to 'Time to Death', 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=3 | older | N=2 | younger | N=1 |
HISTOLOGICAL TYPE | ANOVA test | N=150 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
COMPLETENESS OF RESECTION | ANOVA test | N=28 |
Time to Death | Duration (Months) | 6-149.5 (median=37.4) |
censored | N = 45 | |
death | N = 9 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.94 (12) |
Significant markers | N = 3 | |
pos. correlated | 2 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NPTX1 | -0.6007 | 1.566e-06 | 0.0279 |
TMEM79 | 0.5976 | 1.832e-06 | 0.0326 |
IL20RB | 0.5914 | 2.484e-06 | 0.0443 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 41 | |
MIXED SEROUS AND ENDOMETRIOID | 1 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 12 | |
Significant markers | N = 150 |
ANOVA_P | Q | |
---|---|---|
KLHL34 | 3.401e-17 | 6.06e-13 |
OR4S2 | 1.774e-14 | 3.16e-10 |
C19ORF12 | 2.167e-13 | 3.86e-09 |
TSP50 | 3.379e-13 | 6.02e-09 |
KIAA1324 | 4.24e-13 | 7.55e-09 |
PNOC | 6.89e-13 | 1.23e-08 |
FOXA2 | 2.187e-12 | 3.9e-08 |
CDH6 | 4.379e-12 | 7.8e-08 |
CLDN6 | 9.875e-12 | 1.76e-07 |
SLC6A12 | 6.547e-11 | 1.17e-06 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 25 | |
YES | 29 | |
Significant markers | N = 0 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 39 | |
R1 | 6 | |
R2 | 2 | |
RX | 1 | |
Significant markers | N = 28 |
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Expresson data file = UCEC-TP.medianexp.txt
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Clinical data file = UCEC-TP.merged_data.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.
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.