(primary solid tumor cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18627 genes and 5 clinical features across 369 samples, statistically thresholded by Q value < 0.05, 5 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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319 genes correlated to 'AGE'.
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DIO2|1734 , FAM107A|11170 , MGAT4A|11320 , AEN|64782 , HIF3A|64344 , ...
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3163 genes correlated to 'HISTOLOGICAL.TYPE'.
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L1CAM|3897 , KIAA1324|57535 , CLDN6|9074 , SPDEF|25803 , GRB7|2886 , ...
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2 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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C8ORF79|57604 , CEP68|23177
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2 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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DGCR6|8214 , FRMD1|79981
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=319 | older | N=195 | younger | N=124 |
HISTOLOGICAL TYPE | ANOVA test | N=3163 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=2 | yes | N=2 | no | N=0 |
COMPLETENESS OF RESECTION | ANOVA test | N=2 |
Time to Death | Duration (Months) | 0-187.1 (median=17.9) |
censored | N = 335 | |
death | N = 32 | |
Significant markers | N = 1 | |
associated with shorter survival | 1 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
KCNK10|54207 | 1.78 | 1.546e-06 | 0.029 | 0.728 |
AGE | Mean (SD) | 63.22 (11) |
Significant markers | N = 319 | |
pos. correlated | 195 | |
neg. correlated | 124 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
DIO2|1734 | -0.4127 | 1.316e-16 | 2.45e-12 |
FAM107A|11170 | 0.3632 | 6.025e-13 | 1.12e-08 |
MGAT4A|11320 | 0.3632 | 6.027e-13 | 1.12e-08 |
AEN|64782 | -0.3595 | 1.071e-12 | 1.99e-08 |
HIF3A|64344 | 0.3624 | 1.116e-12 | 2.08e-08 |
NR2F6|2063 | 0.3473 | 6.671e-12 | 1.24e-07 |
S100A1|6271 | 0.3453 | 9.071e-12 | 1.69e-07 |
DACT1|51339 | -0.3447 | 9.894e-12 | 1.84e-07 |
HTRA1|5654 | -0.3371 | 2.933e-11 | 5.46e-07 |
PTGS1|5742 | 0.3368 | 3.085e-11 | 5.74e-07 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 302 | |
MIXED SEROUS AND ENDOMETRIOID | 10 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 57 | |
Significant markers | N = 3163 |
ANOVA_P | Q | |
---|---|---|
L1CAM|3897 | 1.306e-50 | 2.43e-46 |
KIAA1324|57535 | 1.681e-48 | 3.13e-44 |
CLDN6|9074 | 1.448e-40 | 2.7e-36 |
SPDEF|25803 | 2.902e-37 | 5.41e-33 |
GRB7|2886 | 3.992e-37 | 7.43e-33 |
TFF3|7033 | 1.431e-35 | 2.67e-31 |
SLC6A12|6539 | 3.643e-35 | 6.78e-31 |
DLGAP3|58512 | 1.265e-34 | 2.35e-30 |
HIF3A|64344 | 7.629e-34 | 1.42e-29 |
FOXA2|3170 | 3.298e-33 | 6.14e-29 |
2 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 123 | |
YES | 246 | |
Significant markers | N = 2 | |
Higher in YES | 2 | |
Higher in NO | 0 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
C8ORF79|57604 | 5.11 | 6.82e-07 | 0.0127 | 0.6602 |
CEP68|23177 | 4.85 | 2.212e-06 | 0.0412 | 0.6444 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 261 | |
R1 | 21 | |
R2 | 12 | |
RX | 22 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
DGCR6|8214 | 6.398e-10 | 1.19e-05 |
FRMD1|79981 | 1.638e-08 | 0.000305 |
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Expresson data file = UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = UCEC-TP.clin.merged.picked.txt
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Number of patients = 369
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Number of genes = 18627
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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.