This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features.
Testing the association between 554 miRs and 7 clinical features across 504 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one miRs.
-
5 miRs correlated to 'Time to Death'.
-
HSA-MIR-34A , HSA-LET-7G , HSA-MIR-628 , HSA-MIR-497 , HSA-MIR-576
-
72 miRs correlated to 'AGE'.
-
HSA-MIR-424 , HSA-MIR-1247 , HSA-MIR-199A-1 , HSA-MIR-337 , HSA-MIR-34A , ...
-
135 miRs correlated to 'HISTOLOGICAL.TYPE'.
-
HSA-MIR-9-3 , HSA-MIR-9-2 , HSA-MIR-9-1 , HSA-MIR-934 , HSA-MIR-34A , ...
-
18 miRs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
HSA-MIR-3613 , HSA-MIR-128-1 , HSA-MIR-628 , HSA-MIR-103-1 , HSA-MIR-181D , ...
-
33 miRs correlated to 'RACE'.
-
HSA-MIR-92A-1 , HSA-MIR-3170 , HSA-MIR-1304 , HSA-MIR-628 , HSA-MIR-103-1 , ...
-
No miRs correlated to 'COMPLETENESS.OF.RESECTION', and '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=5 | shorter survival | N=0 | longer survival | N=5 |
AGE | Spearman correlation test | N=72 | older | N=9 | younger | N=63 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=135 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=18 | yes | N=18 | no | N=0 |
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 | ||||
RACE | Kruskal-Wallis test | N=33 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0-191.8 (median=22.9) |
censored | N = 445 | |
death | N = 57 | |
Significant markers | N = 5 | |
associated with shorter survival | 0 | |
associated with longer survival | 5 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-34A | 0.72 | 8.038e-05 | 0.045 | 0.368 |
HSA-LET-7G | 0.57 | 0.0001973 | 0.11 | 0.353 |
HSA-MIR-628 | 0.72 | 0.0002753 | 0.15 | 0.375 |
HSA-MIR-497 | 0.72 | 0.0003133 | 0.17 | 0.365 |
HSA-MIR-576 | 0.63 | 0.0005498 | 0.3 | 0.37 |
AGE | Mean (SD) | 63.75 (11) |
Significant markers | N = 72 | |
pos. correlated | 9 | |
neg. correlated | 63 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-424 | -0.315 | 4.765e-13 | 2.64e-10 |
HSA-MIR-1247 | -0.2611 | 3.193e-09 | 1.77e-06 |
HSA-MIR-199A-1 | -0.2369 | 7.588e-08 | 4.19e-05 |
HSA-MIR-337 | -0.2361 | 8.43e-08 | 4.64e-05 |
HSA-MIR-34A | -0.2339 | 1.117e-07 | 6.14e-05 |
HSA-MIR-214 | -0.2327 | 1.346e-07 | 7.39e-05 |
HSA-MIR-199A-2 | -0.2316 | 1.501e-07 | 8.22e-05 |
HSA-MIR-199B | -0.2264 | 2.869e-07 | 0.000157 |
HSA-MIR-3920 | -0.3046 | 4.283e-07 | 0.000234 |
HSA-MIR-409 | -0.2212 | 5.42e-07 | 0.000295 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 383 | |
MIXED SEROUS AND ENDOMETRIOID | 21 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 100 | |
Significant markers | N = 135 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-9-3 | 1.401e-29 | 7.76e-27 |
HSA-MIR-9-2 | 1.587e-27 | 8.77e-25 |
HSA-MIR-9-1 | 1.697e-27 | 9.37e-25 |
HSA-MIR-934 | 1.605e-23 | 8.84e-21 |
HSA-MIR-34A | 5.154e-21 | 2.83e-18 |
HSA-MIR-375 | 4.426e-20 | 2.43e-17 |
HSA-MIR-221 | 2.009e-19 | 1.1e-16 |
HSA-MIR-548V | 7.442e-18 | 4.07e-15 |
HSA-MIR-195 | 1.565e-17 | 8.54e-15 |
HSA-MIR-190B | 1.788e-17 | 9.74e-15 |
18 miRs related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 134 | |
YES | 370 | |
Significant markers | N = 18 | |
Higher in YES | 18 | |
Higher in NO | 0 |
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-3613 | 16402 | 6.374e-09 | 3.53e-06 | 0.6692 |
HSA-MIR-128-1 | 31768 | 1.362e-06 | 0.000753 | 0.6407 |
HSA-MIR-628 | 17838 | 1.777e-06 | 0.000981 | 0.6392 |
HSA-MIR-103-1 | 31682 | 1.834e-06 | 0.00101 | 0.639 |
HSA-MIR-181D | 31397 | 4.793e-06 | 0.00264 | 0.6333 |
HSA-MIR-3170 | 17587 | 7.184e-06 | 0.00394 | 0.6317 |
HSA-MIR-128-2 | 31207 | 8.908e-06 | 0.00488 | 0.6294 |
HSA-MIR-361 | 31118 | 1.184e-05 | 0.00648 | 0.6276 |
HSA-MIR-660 | 31025 | 1.588e-05 | 0.00867 | 0.6258 |
HSA-MIR-210 | 18656 | 2.174e-05 | 0.0118 | 0.6237 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 349 | |
R1 | 22 | |
R2 | 16 | |
RX | 30 | |
Significant markers | N = 0 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 4 | |
ASIAN | 19 | |
BLACK OR AFRICAN AMERICAN | 91 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 9 | |
WHITE | 355 | |
Significant markers | N = 33 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-92A-1 | 3.036e-08 | 1.68e-05 |
HSA-MIR-3170 | 4.698e-08 | 2.6e-05 |
HSA-MIR-1304 | 2.903e-07 | 0.00016 |
HSA-MIR-628 | 3.611e-06 | 0.00199 |
HSA-MIR-103-1 | 4.502e-06 | 0.00248 |
HSA-MIR-20A | 6.831e-06 | 0.00375 |
HSA-MIR-101-2 | 9.06e-06 | 0.00497 |
HSA-MIR-23B | 9.921e-06 | 0.00543 |
HSA-MIR-361 | 1.071e-05 | 0.00585 |
HSA-MIR-199B | 2.429e-05 | 0.0132 |
-
Expresson data file = UCEC-TP.miRseq_RPKM_log2.txt
-
Clinical data file = UCEC-TP.merged_data.txt
-
Number of patients = 504
-
Number of miRs = 554
-
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.