(primary solid tumor cohort)
This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 471 genes and 8 clinical features across 480 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.
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60 genes correlated to 'Time to Death'.
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HSA-MIR-130B , HSA-MIR-223 , HSA-MIR-21 , HSA-MIR-34C , HSA-MIR-138-1 , ...
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2 genes correlated to 'AGE'.
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HSA-MIR-148A , HSA-MIR-590
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12 genes correlated to 'GENDER'.
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HSA-MIR-100 , HSA-MIR-455 , HSA-MIR-708 , HSA-MIR-599 , HSA-MIR-30A , ...
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35 genes correlated to 'PATHOLOGY.T'.
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HSA-MIR-139 , HSA-MIR-625 , HSA-MIR-21 , HSA-MIR-130B , HSA-MIR-486 , ...
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18 genes correlated to 'PATHOLOGICSPREAD(M)'.
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HSA-MIR-193A , HSA-MIR-625 , HSA-MIR-155 , HSA-MIR-28 , HSA-MIR-130B , ...
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41 genes correlated to 'TUMOR.STAGE'.
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HSA-MIR-139 , HSA-MIR-21 , HSA-MIR-155 , HSA-MIR-625 , HSA-MIR-144 , ...
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No genes correlated to '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 | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=60 | shorter survival | N=54 | longer survival | N=6 |
AGE | Spearman correlation test | N=2 | older | N=2 | younger | N=0 |
GENDER | t test | N=12 | male | N=4 | female | N=8 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=35 | higher pT | N=27 | lower pT | N=8 |
PATHOLOGY N | t test | N=0 | ||||
PATHOLOGICSPREAD(M) | t test | N=18 | m1 | N=14 | m0 | N=4 |
TUMOR STAGE | Spearman correlation test | N=41 | higher stage | N=32 | lower stage | N=9 |
Time to Death | Duration (Months) | 0.1-111 (median=35.2) |
censored | N = 323 | |
death | N = 154 | |
Significant markers | N = 60 | |
associated with shorter survival | 54 | |
associated with longer survival | 6 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-130B | 2.1 | 7.949e-14 | 3.7e-11 | 0.665 |
HSA-MIR-223 | 1.63 | 5.21e-13 | 2.4e-10 | 0.649 |
HSA-MIR-21 | 2 | 1.109e-09 | 5.2e-07 | 0.657 |
HSA-MIR-34C | 1.27 | 2.752e-09 | 1.3e-06 | 0.633 |
HSA-MIR-138-1 | 1.38 | 2.552e-08 | 1.2e-05 | 0.644 |
HSA-MIR-1248 | 1.4 | 3.509e-08 | 1.6e-05 | 0.62 |
HSA-MIR-365-2 | 1.66 | 4.286e-08 | 2e-05 | 0.628 |
HSA-MIR-18A | 1.55 | 5.002e-08 | 2.3e-05 | 0.622 |
HSA-MIR-10B | 0.57 | 9.608e-08 | 4.4e-05 | 0.373 |
HSA-MIR-101-1 | 0.55 | 1.142e-07 | 5.3e-05 | 0.395 |
AGE | Mean (SD) | 60.58 (12) |
Significant markers | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-148A | 0.1852 | 4.477e-05 | 0.0211 |
HSA-MIR-590 | 0.1823 | 5.91e-05 | 0.0278 |
GENDER | Labels | N |
FEMALE | 163 | |
MALE | 317 | |
Significant markers | N = 12 | |
Higher in MALE | 4 | |
Higher in FEMALE | 8 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-100 | 8.54 | 6.562e-16 | 3.09e-13 | 0.7423 |
HSA-MIR-455 | -5.26 | 2.457e-07 | 0.000115 | 0.6499 |
HSA-MIR-708 | 5.24 | 3.051e-07 | 0.000143 | 0.6535 |
HSA-MIR-599 | -5.25 | 3.079e-07 | 0.000144 | 0.6756 |
HSA-MIR-30A | -4.34 | 1.875e-05 | 0.00875 | 0.6129 |
HSA-MIR-500B | -4.32 | 2.054e-05 | 0.00957 | 0.6203 |
HSA-MIR-30C-2 | -4.32 | 2.063e-05 | 0.00959 | 0.6125 |
HSA-MIR-31 | 4.17 | 3.961e-05 | 0.0184 | 0.6225 |
HSA-MIR-3934 | 4.06 | 6.878e-05 | 0.0318 | 0.6286 |
HSA-MIR-204 | -4.02 | 7.103e-05 | 0.0328 | 0.6349 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 88.33 (23) |
Score | N | |
0 | 2 | |
70 | 1 | |
80 | 3 | |
90 | 13 | |
100 | 17 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 1.92 (0.97) |
N | ||
T1 | 233 | |
T2 | 62 | |
T3 | 174 | |
T4 | 11 | |
Significant markers | N = 35 | |
pos. correlated | 27 | |
neg. correlated | 8 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-139 | -0.3342 | 5.503e-14 | 2.59e-11 |
HSA-MIR-625 | 0.2793 | 4.732e-10 | 2.22e-07 |
HSA-MIR-21 | 0.2765 | 7.164e-10 | 3.36e-07 |
HSA-MIR-130B | 0.2577 | 1.017e-08 | 4.76e-06 |
HSA-MIR-486 | -0.253 | 1.903e-08 | 8.88e-06 |
HSA-MIR-155 | 0.2529 | 1.925e-08 | 8.97e-06 |
HSA-MIR-144 | -0.2463 | 4.571e-08 | 2.13e-05 |
HSA-MIR-9-2 | 0.2257 | 5.838e-07 | 0.000271 |
HSA-MIR-451 | -0.2239 | 7.202e-07 | 0.000333 |
HSA-MIR-9-1 | 0.2216 | 9.423e-07 | 0.000435 |
PATHOLOGY.N | Labels | N |
N0 | 222 | |
N1 | 17 | |
Significant markers | N = 0 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 405 | |
M1 | 75 | |
Significant markers | N = 18 | |
Higher in M1 | 14 | |
Higher in M0 | 4 |
T(pos if higher in 'M1') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-193A | 5.78 | 3.13e-08 | 1.47e-05 | 0.6467 |
HSA-MIR-625 | 5.36 | 4.97e-07 | 0.000234 | 0.6849 |
HSA-MIR-155 | 5.17 | 1.072e-06 | 0.000503 | 0.6815 |
HSA-MIR-28 | 5.16 | 1.113e-06 | 0.000521 | 0.6609 |
HSA-MIR-130B | 5.12 | 1.218e-06 | 0.000569 | 0.6671 |
HSA-MIR-144 | -5.01 | 2.339e-06 | 0.00109 | 0.6793 |
HSA-MIR-27A | 4.93 | 2.378e-06 | 0.00111 | 0.6328 |
HSA-MIR-106B | 4.86 | 3.123e-06 | 0.00145 | 0.6525 |
HSA-MIR-139 | -4.62 | 1.123e-05 | 0.0052 | 0.6657 |
HSA-MIR-21 | 4.5 | 1.605e-05 | 0.00741 | 0.6393 |
TUMOR.STAGE | Mean (SD) | 2.11 (1.2) |
N | ||
Stage 1 | 229 | |
Stage 2 | 50 | |
Stage 3 | 122 | |
Stage 4 | 79 | |
Significant markers | N = 41 | |
pos. correlated | 32 | |
neg. correlated | 9 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-139 | -0.3474 | 4.64e-15 | 2.19e-12 |
HSA-MIR-21 | 0.2797 | 4.449e-10 | 2.09e-07 |
HSA-MIR-155 | 0.278 | 5.723e-10 | 2.68e-07 |
HSA-MIR-625 | 0.2763 | 7.378e-10 | 3.45e-07 |
HSA-MIR-144 | -0.272 | 1.381e-09 | 6.45e-07 |
HSA-MIR-486 | -0.2666 | 2.975e-09 | 1.39e-06 |
HSA-MIR-451 | -0.2491 | 3.201e-08 | 1.49e-05 |
HSA-MIR-130B | 0.2456 | 5.006e-08 | 2.32e-05 |
HSA-MIR-10B | -0.2324 | 2.617e-07 | 0.000121 |
HSA-MIR-9-2 | 0.232 | 2.746e-07 | 0.000127 |
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Expresson data file = KIRC-TP.miRseq_RPKM_log2.txt
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Clinical data file = KIRC-TP.clin.merged.picked.txt
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Number of patients = 480
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Number of genes = 471
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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 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.