(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 510 genes and 8 clinical features across 848 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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2 genes correlated to 'Time to Death'.
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HSA-MIR-874 , HSA-MIR-148B
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28 genes correlated to 'AGE'.
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HSA-MIR-424 , HSA-MIR-381 , HSA-MIR-31 , HSA-MIR-598 , HSA-MIR-542 , ...
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7 genes correlated to 'LYMPH.NODE.METASTASIS'.
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HSA-MIR-874 , HSA-MIR-374C , HSA-MIR-328 , HSA-MIR-326 , HSA-MIR-197 , ...
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11 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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HSA-MIR-143 , HSA-MIR-210 , HSA-LET-7F-2 , HSA-MIR-200A , HSA-MIR-338 , ...
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No genes correlated to 'GENDER', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'DISTANT.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.
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=2 | shorter survival | N=2 | longer survival | N=0 |
AGE | Spearman correlation test | N=28 | older | N=2 | younger | N=26 |
GENDER | t test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
DISTANT METASTASIS | ANOVA test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=7 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=11 |
Time to Death | Duration (Months) | 0-223.4 (median=18.5) |
censored | N = 694 | |
death | N = 95 | |
Significant markers | N = 2 | |
associated with shorter survival | 2 | |
associated with longer survival | 0 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-874 | 1.58 | 7.248e-06 | 0.0037 | 0.606 |
HSA-MIR-148B | 1.8 | 4.365e-05 | 0.022 | 0.629 |
AGE | Mean (SD) | 58.42 (13) |
Significant markers | N = 28 | |
pos. correlated | 2 | |
neg. correlated | 26 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-424 | -0.2256 | 3.078e-11 | 1.57e-08 |
HSA-MIR-381 | -0.2078 | 1.017e-09 | 5.18e-07 |
HSA-MIR-31 | -0.2039 | 3.324e-09 | 1.69e-06 |
HSA-MIR-598 | -0.1981 | 6.079e-09 | 3.08e-06 |
HSA-MIR-542 | -0.1967 | 7.796e-09 | 3.94e-06 |
HSA-MIR-99A | -0.1892 | 2.891e-08 | 1.46e-05 |
HSA-MIR-652 | -0.1768 | 2.235e-07 | 0.000113 |
HSA-LET-7C | -0.1722 | 4.622e-07 | 0.000232 |
HSA-MIR-450B | -0.1633 | 1.803e-06 | 0.000905 |
HSA-MIR-125B-1 | -0.1531 | 7.592e-06 | 0.0038 |
GENDER | Labels | N |
FEMALE | 839 | |
MALE | 9 | |
Significant markers | N = 0 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 210 | |
YES | 638 | |
Significant markers | N = 0 |
DISTANT.METASTASIS | Labels | N |
CM0 (I+) | 2 | |
M0 | 756 | |
M1 | 14 | |
MX | 76 | |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 248 | |
N0 (I+) | 22 | |
N0 (I-) | 128 | |
N0 (MOL+) | 1 | |
N1 | 101 | |
N1A | 126 | |
N1B | 32 | |
N1C | 2 | |
N1MI | 23 | |
N2 | 50 | |
N2A | 50 | |
N3 | 18 | |
N3A | 29 | |
N3B | 2 | |
N3C | 1 | |
NX | 15 | |
Significant markers | N = 7 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-874 | 1.492e-08 | 7.61e-06 |
HSA-MIR-374C | 2.336e-07 | 0.000119 |
HSA-MIR-328 | 7.44e-06 | 0.00378 |
HSA-MIR-326 | 1.194e-05 | 0.00605 |
HSA-MIR-197 | 1.4e-05 | 0.00708 |
HSA-MIR-331 | 2.72e-05 | 0.0137 |
HSA-MIR-574 | 2.995e-05 | 0.0151 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.22 (4.4) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 72 | |
STAGE IA | 64 | |
STAGE IB | 7 | |
STAGE II | 8 | |
STAGE IIA | 289 | |
STAGE IIB | 189 | |
STAGE III | 2 | |
STAGE IIIA | 120 | |
STAGE IIIB | 24 | |
STAGE IIIC | 40 | |
STAGE IV | 14 | |
STAGE TIS | 1 | |
STAGE X | 17 | |
Significant markers | N = 11 |
ANOVA_P | Q | |
---|---|---|
HSA-MIR-143 | 3.311e-09 | 1.69e-06 |
HSA-MIR-210 | 1.467e-08 | 7.47e-06 |
HSA-LET-7F-2 | 3e-07 | 0.000152 |
HSA-MIR-200A | 1.097e-06 | 0.000556 |
HSA-MIR-338 | 1.269e-05 | 0.00642 |
HSA-MIR-374C | 2.413e-05 | 0.0122 |
HSA-MIR-3607 | 2.578e-05 | 0.013 |
HSA-MIR-3653 | 6.027e-05 | 0.0303 |
HSA-MIR-642A | 9.235e-05 | 0.0464 |
HSA-MIR-200B | 9.28e-05 | 0.0465 |
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Expresson data file = BRCA-TP.miRseq_RPKM_log2.txt
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Clinical data file = BRCA-TP.clin.merged.picked.txt
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Number of patients = 848
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Number of genes = 510
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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 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.