This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features.
Testing the association between 518 miRs and 7 clinical features across 80 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 6 clinical features related to at least one miRs.
-
46 miRs correlated to 'Time to Death'.
-
HSA-MIR-29C , HSA-MIR-106B , HSA-MIR-130B , HSA-MIR-664 , HSA-MIR-3170 , ...
-
3 miRs correlated to 'AGE'.
-
HSA-MIR-505 , HSA-MIR-580 , HSA-MIR-361
-
3 miRs correlated to 'NEOPLASM.DISEASESTAGE'.
-
HSA-MIR-130B , HSA-MIR-196B , HSA-MIR-155
-
11 miRs correlated to 'PATHOLOGY.T.STAGE'.
-
HSA-MIR-615 , HSA-MIR-489 , HSA-MIR-130A , HSA-MIR-130B , HSA-MIR-196A-1 , ...
-
1 miR correlated to 'PATHOLOGY.N.STAGE'.
-
HSA-MIR-510
-
2 miRs correlated to 'GENDER'.
-
HSA-MIR-139 , HSA-MIR-3074
-
No miRs correlated to 'ETHNICITY'
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=46 | shorter survival | N=28 | longer survival | N=18 |
AGE | Spearman correlation test | N=3 | older | N=3 | younger | N=0 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=3 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=11 | higher stage | N=9 | lower stage | N=2 |
PATHOLOGY N STAGE | Wilcoxon test | N=1 | class1 | N=1 | class0 | N=0 |
GENDER | Wilcoxon test | N=2 | male | N=2 | female | N=0 |
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 4.1-153.6 (median=36.1) |
censored | N = 52 | |
death | N = 28 | |
Significant markers | N = 46 | |
associated with shorter survival | 28 | |
associated with longer survival | 18 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-29C | 0.57 | 7.836e-08 | 4.1e-05 | 0.191 |
HSA-MIR-106B | 3.3 | 3.854e-07 | 2e-04 | 0.777 |
HSA-MIR-130B | 2.2 | 3.905e-07 | 2e-04 | 0.8 |
HSA-MIR-664 | 0.41 | 5.522e-06 | 0.0028 | 0.235 |
HSA-MIR-3170 | 1.93 | 9.739e-06 | 0.005 | 0.766 |
HSA-MIR-937 | 1.58 | 1.183e-05 | 0.0061 | 0.803 |
HSA-MIR-1307 | 2.9 | 1.25e-05 | 0.0064 | 0.754 |
HSA-MIR-301B | 1.71 | 1.992e-05 | 0.01 | 0.741 |
HSA-MIR-197 | 2 | 2.359e-05 | 0.012 | 0.761 |
HSA-MIR-1255A | 2.6 | 2.382e-05 | 0.012 | 0.762 |
AGE | Mean (SD) | 46.4 (16) |
Significant markers | N = 3 | |
pos. correlated | 3 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-505 | 0.4483 | 3.042e-05 | 0.0158 |
HSA-MIR-580 | 0.4807 | 5.821e-05 | 0.0301 |
HSA-MIR-361 | 0.4242 | 8.809e-05 | 0.0455 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 9 | |
STAGE II | 36 | |
STAGE III | 16 | |
STAGE IV | 16 | |
Significant markers | N = 3 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-130B | 0.0003359 | 0.174 |
HSA-MIR-196B | 0.0004309 | 0.223 |
HSA-MIR-155 | 0.0005793 | 0.299 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.47 (0.98) |
N | ||
1 | 9 | |
2 | 41 | |
3 | 9 | |
4 | 18 | |
Significant markers | N = 11 | |
pos. correlated | 9 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-615 | 0.5087 | 4.313e-06 | 0.00223 |
HSA-MIR-489 | -0.6581 | 1.735e-05 | 0.00897 |
HSA-MIR-130A | 0.453 | 3.515e-05 | 0.0181 |
HSA-MIR-130B | 0.4483 | 4.341e-05 | 0.0224 |
HSA-MIR-196A-1 | 0.4266 | 0.0001095 | 0.0563 |
HSA-MIR-16-2 | 0.4139 | 0.0001829 | 0.0938 |
HSA-MIR-196A-2 | 0.4161 | 0.0002264 | 0.116 |
HSA-MIR-550A-2 | 0.4141 | 0.0002993 | 0.153 |
HSA-MIR-196B | 0.3979 | 0.0003389 | 0.173 |
HSA-MIR-7-1 | 0.3872 | 0.0005039 | 0.256 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 67 | |
class1 | 10 | |
Significant markers | N = 1 | |
Higher in class1 | 1 | |
Higher in class0 | 0 |
W(pos if higher in 'class1') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-510 | 88 | 0.0004845 | 0.243 | 0.8483 |
GENDER | Labels | N |
FEMALE | 49 | |
MALE | 31 | |
Significant markers | N = 2 | |
Higher in MALE | 2 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-139 | 356 | 6.894e-05 | 0.0357 | 0.7656 |
HSA-MIR-3074 | 1133 | 0.0002299 | 0.119 | 0.7459 |
-
Expresson data file = ACC-TP.miRseq_RPKM_log2.txt
-
Clinical data file = ACC-TP.merged_data.txt
-
Number of patients = 80
-
Number of miRs = 518
-
Number of clinical features = 7
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.