This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18174 genes and 8 clinical features across 74 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.
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1 gene correlated to 'AGE'.
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MCCC2|64087
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16 genes correlated to 'GENDER'.
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XIST|7503 , RPS4Y1|6192 , KDM5C|8242 , PRKY|5616 , ZFX|7543 , ...
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43 genes correlated to 'PATHOLOGY.T'.
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UCK2|7371 , PRCC|5546 , MAD2L1|4085 , ACBD6|84320 , EPR1|8475 , ...
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1 gene correlated to 'PATHOLOGY.N'.
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KIAA0664|23277
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1 gene correlated to 'PATHOLOGICSPREAD(M)'.
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CA8|767
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106 genes correlated to 'TUMOR.STAGE'.
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MAD2L1|4085 , UCK2|7371 , PRCC|5546 , EPR1|8475 , GPR19|2842 , ...
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No genes correlated to 'Time to Death', and 'KARNOFSKY.PERFORMANCE.SCORE'.
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=1 | older | N=1 | younger | N=0 |
GENDER | t test | N=16 | male | N=4 | female | N=12 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=43 | higher pT | N=41 | lower pT | N=2 |
PATHOLOGY N | Spearman correlation test | N=1 | higher pN | N=0 | lower pN | N=1 |
PATHOLOGICSPREAD(M) | ANOVA test | N=1 | ||||
TUMOR STAGE | Spearman correlation test | N=106 | higher stage | N=93 | lower stage | N=13 |
Time to Death | Duration (Months) | 0.5-182.7 (median=15.5) |
censored | N = 58 | |
death | N = 13 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 59.75 (13) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MCCC2|64087 | 0.5349 | 1.545e-06 | 0.0281 |
GENDER | Labels | N |
FEMALE | 22 | |
MALE | 52 | |
Significant markers | N = 16 | |
Higher in MALE | 4 | |
Higher in FEMALE | 12 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503 | -12.87 | 1.749e-13 | 3.18e-09 | 0.9812 |
RPS4Y1|6192 | 11.88 | 2.538e-11 | 4.61e-07 | 0.9562 |
KDM5C|8242 | -8.46 | 2.523e-10 | 4.58e-06 | 0.9423 |
PRKY|5616 | 7.2 | 3.165e-08 | 0.000575 | 0.9126 |
ZFX|7543 | -6.71 | 3.323e-08 | 0.000604 | 0.8872 |
KDM6A|7403 | -6.64 | 3.859e-08 | 0.000701 | 0.9065 |
TSIX|9383 | -7.35 | 3.863e-08 | 0.000702 | 0.9274 |
UBA1|7317 | -6.32 | 1.455e-07 | 0.00264 | 0.8741 |
TXLNG|55787 | -6.05 | 1.724e-07 | 0.00313 | 0.8601 |
DYNLT1|6993 | 5.79 | 3.751e-07 | 0.00681 | 0.8523 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 86.36 (29) |
Score | N | |
0 | 1 | |
90 | 5 | |
100 | 5 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 1.86 (0.96) |
N | ||
T1 | 38 | |
T2 | 9 | |
T3 | 26 | |
T4 | 1 | |
Significant markers | N = 43 | |
pos. correlated | 41 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
UCK2|7371 | 0.66 | 1.592e-10 | 2.89e-06 |
PRCC|5546 | 0.5992 | 1.703e-08 | 0.00031 |
MAD2L1|4085 | 0.5921 | 2.761e-08 | 0.000502 |
ACBD6|84320 | 0.5798 | 6.178e-08 | 0.00112 |
EPR1|8475 | 0.5777 | 8.741e-08 | 0.00159 |
CCT3|7203 | 0.5733 | 9.35e-08 | 0.0017 |
NUF2|83540 | 0.5731 | 9.506e-08 | 0.00173 |
PTHLH|5744 | 0.5767 | 1.413e-07 | 0.00257 |
UBE2T|29089 | 0.5666 | 1.421e-07 | 0.00258 |
GPR19|2842 | 0.5732 | 1.425e-07 | 0.00259 |
PATHOLOGY.N | Mean (SD) | 0.59 (0.68) |
N | ||
N0 | 15 | |
N1 | 11 | |
N2 | 3 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
KIAA0664|23277 | -0.7639 | 1.422e-06 | 0.0258 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 46 | |
M1 | 5 | |
MX | 16 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
CA8|767 | 7.982e-08 | 0.00145 |
TUMOR.STAGE | Mean (SD) | 2.02 (1.2) |
N | ||
Stage 1 | 35 | |
Stage 2 | 3 | |
Stage 3 | 20 | |
Stage 4 | 8 | |
Significant markers | N = 106 | |
pos. correlated | 93 | |
neg. correlated | 13 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MAD2L1|4085 | 0.7054 | 3.756e-11 | 6.83e-07 |
UCK2|7371 | 0.6701 | 7.557e-10 | 1.37e-05 |
PRCC|5546 | 0.644 | 5.435e-09 | 9.88e-05 |
EPR1|8475 | 0.6391 | 1.01e-08 | 0.000184 |
GPR19|2842 | 0.6423 | 1.06e-08 | 0.000193 |
TCTA|6988 | -0.6276 | 1.701e-08 | 0.000309 |
ORC6L|23594 | 0.6156 | 3.777e-08 | 0.000686 |
CDCA5|113130 | 0.6149 | 3.956e-08 | 0.000719 |
PTHLH|5744 | 0.6258 | 4.143e-08 | 0.000753 |
TROAP|10024 | 0.6128 | 4.53e-08 | 0.000823 |
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Expresson data file = KIRP-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = KIRP-TP.clin.merged.picked.txt
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Number of patients = 74
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Number of genes = 18174
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Number of clinical features = 8
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 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 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 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.