This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 501 genes and 8 clinical features across 95 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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3 genes correlated to 'Time to Death'.
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HSA-MIR-141 , HSA-MIR-200C , HSA-MIR-937
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1 gene correlated to 'GENDER'.
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HSA-MIR-607
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9 genes correlated to 'PATHOLOGY.T'.
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HSA-MIR-217 , HSA-MIR-216A , HSA-MIR-200A , HSA-MIR-452 , HSA-MIR-224 , ...
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4 genes correlated to 'PATHOLOGICSPREAD(M)'.
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HSA-MIR-3607 , HSA-MIR-3647 , HSA-MIR-1245 , HSA-MIR-1248
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10 genes correlated to 'TUMOR.STAGE'.
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HSA-MIR-200A , HSA-MIR-224 , HSA-MIR-452 , HSA-MIR-216A , HSA-MIR-200B , ...
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No genes correlated to 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', and 'PATHOLOGY.N'.
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=3 | shorter survival | N=3 | longer survival | N=0 |
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=1 | male | N=1 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=9 | higher pT | N=7 | lower pT | N=2 |
PATHOLOGY N | Spearman correlation test | N=0 | ||||
PATHOLOGICSPREAD(M) | ANOVA test | N=4 | ||||
TUMOR STAGE | Spearman correlation test | N=10 | higher stage | N=7 | lower stage | N=3 |
Time to Death | Duration (Months) | 0-182.7 (median=15.7) |
censored | N = 74 | |
death | N = 14 | |
Significant markers | N = 3 | |
associated with shorter survival | 3 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-141 | 1.66 | 1.874e-05 | 0.0094 | 0.764 |
HSA-MIR-200C | 1.55 | 3.4e-05 | 0.017 | 0.75 |
HSA-MIR-937 | 4 | 9.431e-05 | 0.047 | 0.849 |
AGE | Mean (SD) | 60.07 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 28 | |
MALE | 67 | |
Significant markers | N = 1 | |
Higher in MALE | 1 | |
Higher in FEMALE | 0 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-607 | 4.29 | 8.98e-05 | 0.045 | 0.8083 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 87.5 (24) |
Score | N | |
0 | 1 | |
40 | 1 | |
90 | 9 | |
100 | 9 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 1.77 (0.94) |
N | ||
T1 | 54 | |
T2 | 10 | |
T3 | 30 | |
T4 | 1 | |
Significant markers | N = 9 | |
pos. correlated | 7 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-217 | 0.5035 | 5.741e-07 | 0.000288 |
HSA-MIR-216A | 0.6072 | 8.853e-07 | 0.000443 |
HSA-MIR-200A | -0.4681 | 1.725e-06 | 0.000861 |
HSA-MIR-452 | 0.4581 | 3.044e-06 | 0.00152 |
HSA-MIR-224 | 0.4531 | 4.521e-06 | 0.00225 |
HSA-MIR-1293 | 0.4892 | 7.311e-06 | 0.00363 |
HSA-MIR-200B | -0.4362 | 9.915e-06 | 0.00491 |
HSA-MIR-92A-2 | 0.4171 | 2.609e-05 | 0.0129 |
HSA-MIR-184 | 0.4567 | 9.037e-05 | 0.0446 |
PATHOLOGY.N | Mean (SD) | 0.55 (0.71) |
N | ||
N0 | 19 | |
N1 | 10 | |
N2 | 4 | |
Significant markers | N = 0 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 54 | |
M1 | 5 | |
MX | 27 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
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HSA-MIR-3607 | 1.475e-06 | 0.000739 |
HSA-MIR-3647 | 4.108e-06 | 0.00205 |
HSA-MIR-1245 | 9.513e-06 | 0.00475 |
HSA-MIR-1248 | 6.129e-05 | 0.0305 |
TUMOR.STAGE | Mean (SD) | 1.89 (1.1) |
N | ||
Stage 1 | 49 | |
Stage 2 | 5 | |
Stage 3 | 22 | |
Stage 4 | 9 | |
Significant markers | N = 10 | |
pos. correlated | 7 | |
neg. correlated | 3 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-200A | -0.5464 | 6.305e-08 | 3.16e-05 |
HSA-MIR-224 | 0.5374 | 1.355e-07 | 6.78e-05 |
HSA-MIR-452 | 0.5274 | 2.143e-07 | 0.000107 |
HSA-MIR-216A | 0.6346 | 3.347e-07 | 0.000167 |
HSA-MIR-200B | -0.5037 | 8.929e-07 | 0.000444 |
HSA-MIR-217 | 0.5102 | 9.735e-07 | 0.000483 |
HSA-MIR-429 | -0.461 | 8.988e-06 | 0.00445 |
HSA-MIR-92A-2 | 0.4565 | 1.129e-05 | 0.00558 |
HSA-MIR-1293 | 0.4674 | 5.141e-05 | 0.0253 |
HSA-MIR-1269 | 0.449 | 6.006e-05 | 0.0296 |
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Expresson data file = KIRP.miRseq_RPKM_log2.txt
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Clinical data file = KIRP.clin.merged.picked.txt
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Number of patients = 95
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Number of genes = 501
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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.