This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 564 genes and 8 clinical features across 308 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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5 genes correlated to 'Time to Death'.
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HSA-MIR-377 , HSA-MIR-154 , HSA-MIR-493 , HSA-MIR-337 , HSA-MIR-654
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1 gene correlated to 'PATHOLOGY.N'.
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HSA-MIR-195
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5 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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HSA-MIR-1274B , HSA-MIR-3676 , HSA-MIR-374A , HSA-MIR-660 , HSA-MIR-532
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2 genes correlated to 'NEOADJUVANT.THERAPY'.
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HSA-MIR-3676 , HSA-MIR-660
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No genes correlated to 'AGE', 'GENDER', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=5 | shorter survival | N=5 | longer survival | N=0 |
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=0 | ||||
PATHOLOGY N | Spearman correlation test | N=1 | higher pN | N=1 | lower pN | N=0 |
TUMOR STAGE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=5 | yes | N=4 | no | N=1 |
NEOADJUVANT THERAPY | t test | N=2 | yes | N=2 | no | N=0 |
Time to Death | Duration (Months) | 0.1-210.9 (median=15) |
censored | N = 183 | |
death | N = 122 | |
Significant markers | N = 5 | |
associated with shorter survival | 5 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
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HSA-MIR-377 | 1.48 | 2.217e-06 | 0.0013 | 0.634 |
HSA-MIR-154 | 1.46 | 1.031e-05 | 0.0058 | 0.635 |
HSA-MIR-493 | 1.45 | 2.314e-05 | 0.013 | 0.63 |
HSA-MIR-337 | 1.4 | 2.811e-05 | 0.016 | 0.622 |
HSA-MIR-654 | 1.38 | 4.724e-05 | 0.026 | 0.622 |
AGE | Mean (SD) | 61.09 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 86 | |
MALE | 222 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 2.91 (1) |
N | ||
T1 | 24 | |
T2 | 78 | |
T3 | 62 | |
T4 | 103 | |
Significant markers | N = 0 |
PATHOLOGY.N | Mean (SD) | 1.05 (0.96) |
N | ||
N0 | 99 | |
N1 | 32 | |
N2 | 101 | |
N3 | 5 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-195 | 0.2646 | 3.684e-05 | 0.0208 |
TUMOR.STAGE | Mean (SD) | 3.3 (0.98) |
N | ||
Stage 1 | 17 | |
Stage 2 | 46 | |
Stage 3 | 41 | |
Stage 4 | 158 | |
Significant markers | N = 0 |
5 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 77 | |
YES | 231 | |
Significant markers | N = 5 | |
Higher in YES | 4 | |
Higher in NO | 1 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
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HSA-MIR-1274B | 5.58 | 1.256e-07 | 7.08e-05 | 0.696 |
HSA-MIR-3676 | 5.38 | 2.403e-07 | 0.000135 | 0.6658 |
HSA-MIR-374A | -4.63 | 8.368e-06 | 0.0047 | 0.6576 |
HSA-MIR-660 | 4.53 | 1.177e-05 | 0.0066 | 0.6511 |
HSA-MIR-532 | 4.25 | 3.735e-05 | 0.0209 | 0.6495 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 48 | |
YES | 260 | |
Significant markers | N = 2 | |
Higher in YES | 2 | |
Higher in NO | 0 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
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HSA-MIR-3676 | 4.47 | 2.684e-05 | 0.0151 | 0.6653 |
HSA-MIR-660 | 4.12 | 8.748e-05 | 0.0492 | 0.6508 |
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Expresson data file = HNSC.miRseq_RPKM_log2.txt
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Clinical data file = HNSC.clin.merged.picked.txt
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Number of patients = 308
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Number of genes = 564
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Number of clinical features = 8
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.