This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features.
Testing the association between 593 miRs and 14 clinical features across 285 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 9 clinical features related to at least one miRs.
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1 miR correlated to 'Time to Death'.
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HSA-MIR-607
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2 miRs correlated to 'AGE'.
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HSA-MIR-3200 , HSA-MIR-204
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41 miRs correlated to 'PRIMARY.SITE.OF.DISEASE'.
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HSA-MIR-342 , HSA-MIR-150 , HSA-MIR-379 , HSA-MIR-217 , HSA-MIR-136 , ...
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2 miRs correlated to 'PATHOLOGY.T.STAGE'.
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HSA-MIR-1537 , HSA-MIR-582
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2 miRs correlated to 'PATHOLOGY.N.STAGE'.
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HSA-MIR-29A , HSA-MIR-135B
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1 miR correlated to 'MELANOMA.ULCERATION'.
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HSA-MIR-2277
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2 miRs correlated to 'MELANOMA.PRIMARY.KNOWN'.
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HSA-MIR-582 , HSA-MIR-181A-2
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4 miRs correlated to 'BRESLOW.THICKNESS'.
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HSA-MIR-1537 , HSA-MIR-125B-1 , HSA-MIR-1243 , HSA-MIR-100
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1 miR correlated to 'GENDER'.
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HSA-MIR-361
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No miRs correlated to 'Time from Specimen Diagnosis to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', 'RACE', and 'ETHNICITY'.
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of miRs that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant miRs | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time from Specimen Diagnosis to Death | Cox regression test | N=0 | ||||
Time to Death | Cox regression test | N=1 | shorter survival | N=1 | longer survival | N=0 |
AGE | Spearman correlation test | N=2 | older | N=0 | younger | N=2 |
PRIMARY SITE OF DISEASE | Kruskal-Wallis test | N=41 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=0 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=2 | higher stage | N=2 | lower stage | N=0 |
PATHOLOGY N STAGE | Spearman correlation test | N=2 | higher stage | N=2 | lower stage | N=0 |
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
MELANOMA ULCERATION | Wilcoxon test | N=1 | yes | N=1 | no | N=0 |
MELANOMA PRIMARY KNOWN | Wilcoxon test | N=2 | yes | N=2 | no | N=0 |
BRESLOW THICKNESS | Spearman correlation test | N=4 | higher breslow.thickness | N=2 | lower breslow.thickness | N=2 |
GENDER | Wilcoxon test | N=1 | male | N=1 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
No miR related to 'Time from Specimen Diagnosis to Death'.
Table S1. Basic characteristics of clinical feature: 'Time from Specimen Diagnosis to Death'
Time from Specimen Diagnosis to Death | Duration (Months) | 0-142.4 (median=14.6) |
censored | N = 136 | |
death | N = 136 | |
Significant markers | N = 0 |
Table S2. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.2-357.4 (median=47.5) |
censored | N = 142 | |
death | N = 137 | |
Significant markers | N = 1 | |
associated with shorter survival | 1 | |
associated with longer survival | 0 |
Table S3. Get Full Table List of one miR significantly associated with 'Time to Death' by Cox regression test
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
HSA-MIR-607 | 1.37 | 0.0003476 | 0.21 | 0.585 |
Table S4. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 55.65 (15) |
Significant markers | N = 2 | |
pos. correlated | 0 | |
neg. correlated | 2 |
Table S5. Get Full Table List of 2 miRs significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-3200 | -0.2508 | 2.498e-05 | 0.0148 |
HSA-MIR-204 | -0.224 | 0.0001617 | 0.0957 |
Table S6. Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'
PRIMARY.SITE.OF.DISEASE | Labels | N |
DISTANT METASTASIS | 41 | |
PRIMARY TUMOR | 4 | |
REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE | 60 | |
REGIONAL LYMPH NODE | 179 | |
Significant markers | N = 41 |
Table S7. Get Full Table List of top 10 miRs differentially expressed by 'PRIMARY.SITE.OF.DISEASE'
ANOVA_P | Q | |
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HSA-MIR-342 | 7.301e-09 | 4.33e-06 |
HSA-MIR-150 | 1.018e-07 | 6.02e-05 |
HSA-MIR-379 | 1.88e-07 | 0.000111 |
HSA-MIR-217 | 4.272e-07 | 0.000252 |
HSA-MIR-136 | 1.559e-06 | 0.000918 |
HSA-MIR-410 | 1.741e-06 | 0.00102 |
HSA-MIR-654 | 2.119e-06 | 0.00124 |
HSA-MIR-134 | 2.35e-06 | 0.00138 |
HSA-MIR-382 | 3.423e-06 | 0.002 |
HSA-MIR-127 | 3.585e-06 | 0.00209 |
Table S8. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
I OR II NOS | 10 | |
STAGE 0 | 6 | |
STAGE I | 22 | |
STAGE IA | 11 | |
STAGE IB | 25 | |
STAGE II | 16 | |
STAGE IIA | 9 | |
STAGE IIB | 15 | |
STAGE IIC | 10 | |
STAGE III | 30 | |
STAGE IIIA | 13 | |
STAGE IIIB | 26 | |
STAGE IIIC | 50 | |
STAGE IV | 13 | |
Significant markers | N = 0 |
Table S9. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 2.42 (1.3) |
N | ||
0 | 22 | |
1 | 30 | |
2 | 61 | |
3 | 57 | |
4 | 56 | |
Significant markers | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
Table S10. Get Full Table List of 2 miRs significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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HSA-MIR-1537 | 0.3013 | 3.582e-05 | 0.0212 |
HSA-MIR-582 | 0.2536 | 0.0001158 | 0.0686 |
Table S11. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Mean (SD) | 0.88 (1.1) |
N | ||
0 | 142 | |
1 | 51 | |
2 | 34 | |
3 | 38 | |
Significant markers | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
Table S12. Get Full Table List of 2 miRs significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-29A | 0.2226 | 0.0002594 | 0.154 |
HSA-MIR-135B | 0.2186 | 0.0004255 | 0.252 |
Table S13. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 254 | |
M1 | 4 | |
M1A | 2 | |
M1B | 3 | |
M1C | 5 | |
Significant markers | N = 0 |
Table S14. Basic characteristics of clinical feature: 'MELANOMA.ULCERATION'
MELANOMA.ULCERATION | Labels | N |
NO | 104 | |
YES | 74 | |
Significant markers | N = 1 | |
Higher in YES | 1 | |
Higher in NO | 0 |
Table S15. Get Full Table List of one miR differentially expressed by 'MELANOMA.ULCERATION'
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-2277 | 4639 | 0.0003124 | 0.185 | 0.6627 |
Table S16. Basic characteristics of clinical feature: 'MELANOMA.PRIMARY.KNOWN'
MELANOMA.PRIMARY.KNOWN | Labels | N |
NO | 36 | |
YES | 249 | |
Significant markers | N = 2 | |
Higher in YES | 2 | |
Higher in NO | 0 |
Table S17. Get Full Table List of 2 miRs differentially expressed by 'MELANOMA.PRIMARY.KNOWN'
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
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HSA-MIR-582 | 6186 | 0.0002282 | 0.135 | 0.6901 |
HSA-MIR-181A-2 | 6126 | 0.000377 | 0.223 | 0.6834 |
Table S18. Basic characteristics of clinical feature: 'BRESLOW.THICKNESS'
BRESLOW.THICKNESS | Mean (SD) | 3.61 (5.1) |
Significant markers | N = 4 | |
pos. correlated | 2 | |
neg. correlated | 2 |
Table S19. Get Full Table List of 4 miRs significantly correlated to 'BRESLOW.THICKNESS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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HSA-MIR-1537 | 0.3781 | 4.003e-07 | 0.000237 |
HSA-MIR-125B-1 | -0.252 | 0.000249 | 0.147 |
HSA-MIR-1243 | 0.2845 | 0.000254 | 0.15 |
HSA-MIR-100 | -0.2432 | 0.0004138 | 0.244 |
Table S20. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 105 | |
MALE | 180 | |
Significant markers | N = 1 | |
Higher in MALE | 1 | |
Higher in FEMALE | 0 |
Table S21. Get Full Table List of one miR differentially expressed by 'GENDER'. 0 significant gene(s) located in sex chromosomes is(are) filtered out.
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
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HSA-MIR-361 | 6520 | 1.272e-05 | 0.00754 | 0.655 |
Table S22. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
ASIAN | 5 | |
BLACK OR AFRICAN AMERICAN | 1 | |
WHITE | 277 | |
Significant markers | N = 0 |
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Expresson data file = SKCM-TM.miRseq_RPKM_log2.txt
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Clinical data file = SKCM-TM.merged_data.txt
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Number of patients = 285
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Number of miRs = 593
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Number of clinical features = 14
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 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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.