(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 538 genes and 9 clinical features across 134 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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1 gene correlated to 'AGE'.
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HSA-MIR-96
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1 gene correlated to 'HISTOLOGICAL.TYPE'.
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HSA-MIR-33A
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2 genes correlated to 'PATHOLOGY.T'.
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HSA-MIR-200B , HSA-MIR-133B
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5 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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HSA-MIR-3150 , HSA-MIR-23A , HSA-MIR-548F-1 , HSA-MIR-559 , HSA-MIR-1237
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No genes correlated to 'Time to Death', 'GENDER', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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=1 | older | N=1 | younger | N=0 |
GENDER | t test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=1 | ||||
PATHOLOGY T | Spearman correlation test | N=2 | higher pT | N=1 | lower pT | N=1 |
PATHOLOGY N | Spearman correlation test | N=0 | ||||
PATHOLOGICSPREAD(M) | ANOVA test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=5 | yes | N=5 | no | N=0 |
Time to Death | Duration (Months) | 0.1-72.2 (median=3) |
censored | N = 82 | |
death | N = 15 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 68.03 (11) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-96 | 0.3411 | 8.718e-05 | 0.0469 |
GENDER | Labels | N |
FEMALE | 52 | |
MALE | 82 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
STOMACH ADENOCARCINOMA - DIFFUSE TYPE | 14 | |
STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) | 69 | |
STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE | 7 | |
STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE | 3 | |
STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE | 10 | |
STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) | 26 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-33A | 5.164e-05 | 0.0278 |
PATHOLOGY.T | Mean (SD) | 2.63 (0.78) |
N | ||
T1 | 6 | |
T2 | 51 | |
T3 | 50 | |
T4 | 17 | |
Significant markers | N = 2 | |
pos. correlated | 1 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-200B | -0.3848 | 1.019e-05 | 0.00548 |
HSA-MIR-133B | 0.3437 | 9.294e-05 | 0.0499 |
PATHOLOGY.N | Mean (SD) | 1.03 (0.97) |
N | ||
N0 | 43 | |
N1 | 46 | |
N2 | 21 | |
N3 | 13 | |
Significant markers | N = 0 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 114 | |
M1 | 14 | |
MX | 6 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 2.51 (1) |
N | ||
Stage 1 | 24 | |
Stage 2 | 35 | |
Stage 3 | 34 | |
Stage 4 | 25 | |
Significant markers | N = 0 |
5 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 5 | |
YES | 129 | |
Significant markers | N = 5 | |
Higher in YES | 5 | |
Higher in NO | 0 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-3150 | 7.11 | 1.823e-08 | 8.66e-06 | 0.8242 |
HSA-MIR-23A | 8.66 | 2.188e-07 | 0.000104 | 0.8791 |
HSA-MIR-548F-1 | 7.46 | 7.67e-07 | 0.000363 | 0.9074 |
HSA-MIR-559 | 7.32 | 5.957e-06 | 0.00281 | 0.8814 |
HSA-MIR-1237 | 4.77 | 4.818e-05 | 0.0227 | 0.763 |
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Expresson data file = STAD-TP.miRseq_RPKM_log2.txt
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Clinical data file = STAD-TP.clin.merged.picked.txt
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Number of patients = 134
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Number of genes = 538
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Number of clinical features = 9
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.