This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 456 miRs and 9 clinical features across 482 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one miRs.
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66 miRs correlated to 'Time to Death'.
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HSA-MIR-223 , HSA-MIR-130B , HSA-MIR-34C , HSA-MIR-21 , HSA-MIR-10B , ...
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1 miR correlated to 'AGE'.
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HSA-MIR-590
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38 miRs correlated to 'NEOPLASM.DISEASESTAGE'.
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HSA-MIR-139 , HSA-MIR-625 , HSA-MIR-486 , HSA-MIR-21 , HSA-MIR-28 , ...
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32 miRs correlated to 'PATHOLOGY.T.STAGE'.
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HSA-MIR-139 , HSA-MIR-21 , HSA-MIR-486 , HSA-MIR-625 , HSA-MIR-144 , ...
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18 miRs correlated to 'PATHOLOGY.M.STAGE'.
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HSA-MIR-106B , HSA-MIR-193A , HSA-MIR-625 , HSA-MIR-28 , HSA-MIR-155 , ...
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9 miRs correlated to 'GENDER'.
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HSA-MIR-100 , HSA-MIR-708 , HSA-MIR-455 , HSA-MIR-599 , HSA-MIR-30A , ...
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No miRs correlated to 'PATHOLOGY.N.STAGE', 'KARNOFSKY.PERFORMANCE.SCORE', and 'NUMBERPACKYEARSSMOKED'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant miRs | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=66 | shorter survival | N=56 | longer survival | N=10 |
AGE | Spearman correlation test | N=1 | older | N=1 | younger | N=0 |
NEOPLASM DISEASESTAGE | ANOVA test | N=38 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=32 | higher stage | N=23 | lower stage | N=9 |
PATHOLOGY N STAGE | t test | N=0 | ||||
PATHOLOGY M STAGE | t test | N=18 | m1 | N=14 | m0 | N=4 |
GENDER | t test | N=9 | male | N=3 | female | N=6 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.1-120.6 (median=36.5) |
censored | N = 321 | |
death | N = 161 | |
Significant markers | N = 66 | |
associated with shorter survival | 56 | |
associated with longer survival | 10 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-223 | 1.6 | 2.042e-12 | 9.3e-10 | 0.643 |
HSA-MIR-130B | 2 | 4.618e-12 | 2.1e-09 | 0.647 |
HSA-MIR-34C | 1.28 | 1.73e-10 | 7.9e-08 | 0.64 |
HSA-MIR-21 | 2.1 | 1.018e-09 | 4.6e-07 | 0.661 |
HSA-MIR-10B | 0.56 | 1.228e-08 | 5.6e-06 | 0.369 |
HSA-MIR-365-2 | 1.67 | 1.872e-08 | 8.4e-06 | 0.622 |
HSA-MIR-365-1 | 1.64 | 3.725e-08 | 1.7e-05 | 0.619 |
HSA-MIR-18A | 1.54 | 4.235e-08 | 1.9e-05 | 0.617 |
HSA-MIR-1248 | 1.39 | 7.657e-08 | 3.4e-05 | 0.609 |
HSA-MIR-101-1 | 0.58 | 9.034e-08 | 4e-05 | 0.404 |
AGE | Mean (SD) | 60.58 (12) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-590 | 0.1806 | 6.665e-05 | 0.0304 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 228 | |
STAGE II | 52 | |
STAGE III | 124 | |
STAGE IV | 78 | |
Significant markers | N = 38 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-139 | 4.681e-13 | 2.13e-10 |
HSA-MIR-625 | 8.392e-11 | 3.82e-08 |
HSA-MIR-486 | 8.048e-09 | 3.65e-06 |
HSA-MIR-21 | 8.454e-09 | 3.83e-06 |
HSA-MIR-28 | 1.568e-08 | 7.09e-06 |
HSA-MIR-144 | 2.871e-08 | 1.29e-05 |
HSA-LET-7I | 3.454e-08 | 1.55e-05 |
HSA-MIR-155 | 3.554e-08 | 1.6e-05 |
HSA-MIR-130B | 6.128e-08 | 2.75e-05 |
HSA-MIR-10B | 3.356e-07 | 0.00015 |
PATHOLOGY.T.STAGE | Mean (SD) | 1.93 (0.97) |
N | ||
1 | 233 | |
2 | 63 | |
3 | 175 | |
4 | 11 | |
Significant markers | N = 32 | |
pos. correlated | 23 | |
neg. correlated | 9 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-139 | -0.3352 | 4.017e-14 | 1.83e-11 |
HSA-MIR-21 | 0.2754 | 7.702e-10 | 3.5e-07 |
HSA-MIR-486 | -0.2724 | 1.203e-09 | 5.46e-07 |
HSA-MIR-625 | 0.2693 | 1.879e-09 | 8.51e-07 |
HSA-MIR-144 | -0.2481 | 3.392e-08 | 1.53e-05 |
HSA-MIR-155 | 0.2463 | 4.281e-08 | 1.93e-05 |
HSA-MIR-451 | -0.2352 | 1.747e-07 | 7.86e-05 |
HSA-MIR-130B | 0.2315 | 2.774e-07 | 0.000125 |
HSA-MIR-9-1 | 0.2304 | 3.165e-07 | 0.000142 |
HSA-MIR-9-2 | 0.2219 | 8.669e-07 | 0.000387 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 222 | |
class1 | 18 | |
Significant markers | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 405 | |
M1 | 77 | |
Significant markers | N = 18 | |
Higher in M1 | 14 | |
Higher in M0 | 4 |
T(pos if higher in 'M1') | ttestP | Q | AUC | |
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HSA-MIR-106B | 5.67 | 7.499e-08 | 3.42e-05 | 0.6749 |
HSA-MIR-193A | 5.53 | 1.173e-07 | 5.34e-05 | 0.6414 |
HSA-MIR-625 | 5.39 | 4.312e-07 | 0.000196 | 0.6892 |
HSA-MIR-28 | 5.27 | 6.543e-07 | 0.000296 | 0.6603 |
HSA-MIR-155 | 5.26 | 6.851e-07 | 0.00031 | 0.6824 |
HSA-LET-7I | 4.99 | 1.949e-06 | 0.000879 | 0.6613 |
HSA-MIR-130B | 4.98 | 2.115e-06 | 0.000952 | 0.6664 |
HSA-MIR-144 | -4.99 | 2.395e-06 | 0.00108 | 0.676 |
HSA-MIR-139 | -4.82 | 4.818e-06 | 0.00216 | 0.6691 |
HSA-MIR-27A | 4.66 | 7.415e-06 | 0.00331 | 0.6275 |
GENDER | Labels | N |
FEMALE | 163 | |
MALE | 319 | |
Significant markers | N = 9 | |
Higher in MALE | 3 | |
Higher in FEMALE | 6 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-100 | 8.19 | 6.655e-15 | 3.03e-12 | 0.7304 |
HSA-MIR-708 | 5.48 | 8.984e-08 | 4.09e-05 | 0.659 |
HSA-MIR-455 | -5.38 | 1.342e-07 | 6.09e-05 | 0.6599 |
HSA-MIR-599 | -5.16 | 5.008e-07 | 0.000227 | 0.6779 |
HSA-MIR-30A | -4.37 | 1.585e-05 | 0.00716 | 0.6149 |
HSA-MIR-31 | 4.37 | 1.715e-05 | 0.00773 | 0.6296 |
HSA-MIR-30C-2 | -4.16 | 4.06e-05 | 0.0183 | 0.6088 |
HSA-MIR-628 | -3.99 | 7.91e-05 | 0.0355 | 0.5945 |
HSA-MIR-204 | -3.96 | 9.203e-05 | 0.0412 | 0.6356 |
No miR 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 |
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Expresson data file = KIRC-TP.miRseq_RPKM_log2.txt
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Clinical data file = KIRC-TP.merged_data.txt
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Number of patients = 482
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Number of miRs = 456
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Number of clinical features = 9
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.