This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 6 clinical features across 54 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one genes.
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6 genes correlated to 'AGE'.
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NPTX1 , TMEM79 , IL20RB , DLC1 , CDH12 , ...
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39 genes correlated to 'HISTOLOGICAL.TYPE'.
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PNOC , TSP50 , PPAP2C , FOXA2 , ZNF250 , ...
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No genes correlated to 'Time to Death', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'COMPLETENESS.OF.RESECTION', and 'RACE'.
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=0 | ||||
AGE | Spearman correlation test | N=6 | older | N=3 | younger | N=3 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=39 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 | ||||
RACE | Kruskal-Wallis test | N=0 |
Time to Death | Duration (Months) | 6-149.6 (median=37.4) |
censored | N = 45 | |
death | N = 9 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.94 (12) |
Significant markers | N = 6 | |
pos. correlated | 3 | |
neg. correlated | 3 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 41 | |
MIXED SEROUS AND ENDOMETRIOID | 1 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 12 | |
Significant markers | N = 39 |
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 | 41 | |
R1 | 4 | |
R2 | 2 | |
RX | 1 | |
Significant markers | N = 0 |
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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 = 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 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.