(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 564 genes and 6 clinical features across 32 samples, statistically thresholded by Q value < 0.05, 1 clinical feature related to at least one genes.
-
1 gene correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
HSA-MIR-3158-2
-
No genes correlated to 'Time to Death', 'AGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', and 'STOPPEDSMOKINGYEAR'.
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=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
STOPPEDSMOKINGYEAR | Spearman correlation test | N=0 | ||||
TOBACCOSMOKINGHISTORYINDICATOR | Spearman correlation test | N=1 | higher tobaccosmokinghistoryindicator | N=0 | lower tobaccosmokinghistoryindicator | N=1 |
Time to Death | Duration (Months) | 0.1-101.8 (median=5.8) |
censored | N = 27 | |
death | N = 4 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 49.88 (13) |
Significant markers | N = 0 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 8 | |
YES | 24 | |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 17.83 (12) |
Value | N | |
5 | 1 | |
12 | 1 | |
15 | 2 | |
20 | 1 | |
40 | 1 | |
Significant markers | N = 0 |
STOPPEDSMOKINGYEAR | Mean (SD) | 1998 (15) |
Value | N | |
1978 | 1 | |
1995 | 1 | |
2008 | 1 | |
2011 | 1 | |
Significant markers | N = 0 |
One gene related to 'TOBACCOSMOKINGHISTORYINDICATOR'.
TOBACCOSMOKINGHISTORYINDICATOR | Mean (SD) | 1.97 (1.2) |
Value | N | |
1 | 14 | |
2 | 8 | |
3 | 1 | |
4 | 6 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-3158-2 | -0.7442 | 3.059e-05 | 0.0173 |
-
Expresson data file = CESC-TP.miRseq_RPKM_log2.txt
-
Clinical data file = CESC-TP.clin.merged.picked.txt
-
Number of patients = 32
-
Number of genes = 564
-
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 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.