(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 417 genes and 9 clinical features across 407 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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8 genes correlated to 'AGE'.
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HSA-MIR-141 , HSA-MIR-26A-1 , HSA-MIR-153-2 , HSA-MIR-34A , HSA-MIR-432 , ...
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13 genes correlated to 'HISTOLOGICAL.TYPE'.
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HSA-MIR-592 , HSA-MIR-31 , HSA-MIR-92A-1 , HSA-MIR-92A-2 , HSA-MIR-374B , ...
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1 gene correlated to 'PATHOLOGY.T'.
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HSA-MIR-501
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16 genes correlated to 'PATHOLOGICSPREAD(M)'.
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HSA-MIR-628 , HSA-MIR-1180 , HSA-MIR-140 , HSA-MIR-106A , HSA-LET-7F-2 , ...
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1 gene correlated to 'TUMOR.STAGE'.
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HSA-MIR-625
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No genes correlated to 'Time to Death', 'GENDER', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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=8 | older | N=7 | younger | N=1 |
GENDER | t test | N=0 | ||||
HISTOLOGICAL TYPE | t test | N=13 | colon mucinous adenocarcinoma | N=2 | colon adenocarcinoma | N=11 |
PATHOLOGY T | Spearman correlation test | N=1 | higher pT | N=0 | lower pT | N=1 |
PATHOLOGY N | Spearman correlation test | N=0 | ||||
PATHOLOGICSPREAD(M) | ANOVA test | N=16 | ||||
TUMOR STAGE | Spearman correlation test | N=1 | higher stage | N=0 | lower stage | N=1 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 |
Time to Death | Duration (Months) | 0.1-135.5 (median=7.5) |
censored | N = 260 | |
death | N = 49 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 67.29 (13) |
Significant markers | N = 8 | |
pos. correlated | 7 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-141 | 0.2362 | 1.484e-06 | 0.000619 |
HSA-MIR-26A-1 | 0.2238 | 5.295e-06 | 0.0022 |
HSA-MIR-153-2 | 0.2191 | 8.38e-06 | 0.00348 |
HSA-MIR-34A | 0.2147 | 1.283e-05 | 0.00531 |
HSA-MIR-432 | -0.2118 | 1.94e-05 | 0.00801 |
HSA-MIR-33B | 0.1961 | 7.079e-05 | 0.0292 |
HSA-MIR-616 | 0.1945 | 9.184e-05 | 0.0377 |
HSA-MIR-653 | 0.1932 | 0.0001073 | 0.044 |
GENDER | Labels | N |
FEMALE | 192 | |
MALE | 215 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
COLON ADENOCARCINOMA | 349 | |
COLON MUCINOUS ADENOCARCINOMA | 55 | |
Significant markers | N = 13 | |
Higher in COLON MUCINOUS ADENOCARCINOMA | 2 | |
Higher in COLON ADENOCARCINOMA | 11 |
T(pos if higher in 'COLON MUCINOUS ADENOCARCINOMA') | ttestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-592 | -6.31 | 1.886e-08 | 7.87e-06 | 0.746 |
HSA-MIR-31 | 5.81 | 1.242e-07 | 5.17e-05 | 0.7159 |
HSA-MIR-92A-1 | -5.59 | 3.277e-07 | 0.000136 | 0.714 |
HSA-MIR-92A-2 | -4.83 | 7.505e-06 | 0.00311 | 0.6961 |
HSA-MIR-374B | -4.78 | 7.745e-06 | 0.0032 | 0.6792 |
HSA-MIR-196B | -4.77 | 9.22e-06 | 0.0038 | 0.686 |
HSA-MIR-574 | 4.64 | 1.48e-05 | 0.00608 | 0.6868 |
HSA-MIR-29A | -4.63 | 1.666e-05 | 0.00683 | 0.6971 |
HSA-MIR-1247 | -4.61 | 1.728e-05 | 0.00707 | 0.6913 |
HSA-MIR-98 | -4.53 | 2.086e-05 | 0.00851 | 0.6802 |
PATHOLOGY.T | Mean (SD) | 2.88 (0.63) |
N | ||
T0 | 1 | |
T1 | 10 | |
T2 | 69 | |
T3 | 279 | |
T4 | 45 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-501 | -0.1908 | 0.0001139 | 0.0475 |
PATHOLOGY.N | Mean (SD) | 0.58 (0.77) |
N | ||
N0 | 241 | |
N1 | 94 | |
N2 | 70 | |
Significant markers | N = 0 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 305 | |
M1 | 50 | |
M1A | 7 | |
M1B | 1 | |
MX | 36 | |
Significant markers | N = 16 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-628 | 1.496e-06 | 0.000624 |
HSA-MIR-1180 | 1.503e-06 | 0.000625 |
HSA-MIR-140 | 1.926e-06 | 0.000799 |
HSA-MIR-106A | 4.51e-06 | 0.00187 |
HSA-LET-7F-2 | 5.673e-06 | 0.00234 |
HSA-MIR-142 | 7.536e-06 | 0.0031 |
HSA-MIR-301A | 1.422e-05 | 0.00585 |
HSA-LET-7A-1 | 2.684e-05 | 0.011 |
HSA-MIR-126 | 2.76e-05 | 0.0113 |
HSA-MIR-1277 | 2.984e-05 | 0.0122 |
TUMOR.STAGE | Mean (SD) | 2.42 (0.93) |
N | ||
Stage 1 | 65 | |
Stage 2 | 155 | |
Stage 3 | 113 | |
Stage 4 | 57 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-625 | -0.2101 | 2.892e-05 | 0.0121 |
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Expresson data file = COAD-TP.miRseq_RPKM_log2.txt
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Clinical data file = COAD-TP.clin.merged.picked.txt
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Number of patients = 407
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Number of genes = 417
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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.