This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 543 miRs and 6 clinical features across 348 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one miRs.
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31 miRs correlated to 'Time to Death'.
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HSA-MIR-155 , HSA-MIR-10A , HSA-MIR-15B , HSA-MIR-346 , HSA-MIR-196B , ...
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23 miRs correlated to 'AGE'.
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HSA-MIR-34A , HSA-MIR-155 , HSA-MIR-25 , HSA-MIR-10A , HSA-MIR-146A , ...
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56 miRs correlated to 'HISTOLOGICAL.TYPE'.
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HSA-MIR-1262 , HSA-MIR-186 , HSA-MIR-3074 , HSA-MIR-3065 , HSA-MIR-219-1 , ...
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25 miRs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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HSA-MIR-628 , HSA-MIR-1274B , HSA-MIR-3130-1 , HSA-MIR-30E , HSA-MIR-296 , ...
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No miRs correlated to 'GENDER', and 'KARNOFSKY.PERFORMANCE.SCORE'.
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=31 | shorter survival | N=28 | longer survival | N=3 |
AGE | Spearman correlation test | N=23 | older | N=19 | younger | N=4 |
GENDER | t test | N=0 | ||||
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=56 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=25 | yes | N=3 | no | N=22 |
Time to Death | Duration (Months) | 0-211.2 (median=14.9) |
censored | N = 280 | |
death | N = 67 | |
Significant markers | N = 31 | |
associated with shorter survival | 28 | |
associated with longer survival | 3 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-155 | 1.91 | 1.644e-12 | 8.9e-10 | 0.781 |
HSA-MIR-10A | 1.33 | 6.747e-11 | 3.7e-08 | 0.72 |
HSA-MIR-15B | 1.87 | 3.41e-09 | 1.8e-06 | 0.786 |
HSA-MIR-346 | 0.61 | 5.45e-09 | 2.9e-06 | 0.338 |
HSA-MIR-196B | 1.22 | 1.04e-08 | 5.6e-06 | 0.713 |
HSA-MIR-148A | 1.57 | 5.738e-08 | 3.1e-05 | 0.747 |
HSA-MIR-9-1 | 0.42 | 1.759e-07 | 9.4e-05 | 0.244 |
HSA-MIR-9-2 | 0.42 | 1.788e-07 | 9.6e-05 | 0.244 |
HSA-MIR-21 | 1.45 | 4.3e-07 | 0.00023 | 0.715 |
HSA-MIR-944 | 1.55 | 2.126e-06 | 0.0011 | 0.79 |
AGE | Mean (SD) | 43.47 (14) |
Significant markers | N = 23 | |
pos. correlated | 19 | |
neg. correlated | 4 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-34A | 0.3429 | 4.9e-11 | 2.66e-08 |
HSA-MIR-155 | 0.2893 | 3.895e-08 | 2.11e-05 |
HSA-MIR-25 | 0.2804 | 1.038e-07 | 5.62e-05 |
HSA-MIR-10A | 0.2609 | 8.032e-07 | 0.000434 |
HSA-MIR-146A | 0.253 | 1.739e-06 | 0.000937 |
HSA-MIR-2115 | 0.2632 | 1.946e-06 | 0.00105 |
HSA-MIR-10B | 0.2515 | 2.016e-06 | 0.00108 |
HSA-MIR-126 | 0.2492 | 2.529e-06 | 0.00136 |
HSA-MIR-664 | 0.2455 | 4.778e-06 | 0.00256 |
HSA-MIR-429 | 0.2836 | 6.491e-06 | 0.00347 |
GENDER | Labels | N |
FEMALE | 160 | |
MALE | 188 | |
Significant markers | N = 0 |
No miR related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 87.97 (12) |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ASTROCYTOMA | 118 | |
OLIGOASTROCYTOMA | 95 | |
OLIGODENDROGLIOMA | 135 | |
Significant markers | N = 56 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-1262 | 2.444e-15 | 1.33e-12 |
HSA-MIR-186 | 3.074e-13 | 1.67e-10 |
HSA-MIR-3074 | 1.106e-11 | 5.98e-09 |
HSA-MIR-3065 | 1.625e-11 | 8.78e-09 |
HSA-MIR-219-1 | 2.366e-11 | 1.28e-08 |
HSA-MIR-592 | 3.29e-11 | 1.77e-08 |
HSA-MIR-576 | 3.059e-10 | 1.64e-07 |
HSA-MIR-301A | 8.364e-10 | 4.48e-07 |
HSA-MIR-21 | 2.864e-09 | 1.53e-06 |
HSA-MIR-23A | 4.749e-09 | 2.54e-06 |
25 miRs related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 88 | |
YES | 260 | |
Significant markers | N = 25 | |
Higher in YES | 3 | |
Higher in NO | 22 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-628 | -6.37 | 1.771e-09 | 9.62e-07 | 0.7174 |
HSA-MIR-1274B | -5.96 | 1.193e-08 | 6.47e-06 | 0.6909 |
HSA-MIR-3130-1 | -5.7 | 6.832e-08 | 3.7e-05 | 0.7044 |
HSA-MIR-30E | -5.39 | 2.118e-07 | 0.000114 | 0.687 |
HSA-MIR-296 | -5.23 | 4.783e-07 | 0.000258 | 0.663 |
HSA-MIR-30C-1 | -5.14 | 6.251e-07 | 0.000336 | 0.6544 |
HSA-MIR-424 | -5.14 | 9.368e-07 | 0.000503 | 0.6903 |
HSA-MIR-331 | -5 | 1.255e-06 | 0.000673 | 0.6535 |
HSA-MIR-32 | -4.94 | 2.151e-06 | 0.00115 | 0.6648 |
HSA-MIR-3613 | -4.87 | 2.674e-06 | 0.00143 | 0.6552 |
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Expresson data file = LGG-TP.miRseq_RPKM_log2.txt
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Clinical data file = LGG-TP.merged_data.txt
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Number of patients = 348
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Number of miRs = 543
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Number of clinical features = 6
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.
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.