This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 18086 genes and 14 clinical features across 285 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.
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645 genes correlated to 'Time from Specimen Diagnosis to Death'.
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SAMSN1|64092 , CXCL10|3627 , EAF2|55840 , GBP5|115362 , LAG3|3902 , ...
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18 genes correlated to 'AGE'.
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ACOX2|8309 , CMBL|134147 , FAM84B|157638 , MAOB|4129 , MGST2|4258 , ...
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261 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
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C7|730 , SHISA3|152573 , RBP5|83758 , FOXF1|2294 , TMEM156|80008 , ...
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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RAI14|26064 , SEMA3E|9723
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10 genes correlated to 'PATHOLOGY.T.STAGE'.
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INHA|3623 , TNFSF13B|10673 , GBP4|115361 , LOXL4|84171 , ANKRD22|118932 , ...
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7 genes correlated to 'PATHOLOGY.N.STAGE'.
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C12ORF62|84987 , PTPRG|5793 , IL17RD|54756 , MAML3|55534 , TMEM208|29100 , ...
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73 genes correlated to 'BRESLOW.THICKNESS'.
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TNFSF13B|10673 , GBP4|115361 , SLC7A8|23428 , ATP6V0A1|535 , FGL2|10875 , ...
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5 genes correlated to 'GENDER'.
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CYORF15A|246126 , HDHD1A|8226 , NCRNA00183|554203 , CYORF15B|84663 , CA5BP|340591
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No genes correlated to 'Time to Death', 'PATHOLOGY.M.STAGE', 'MELANOMA.ULCERATION', 'MELANOMA.PRIMARY.KNOWN', '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 genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time from Specimen Diagnosis to Death | Cox regression test | N=645 | shorter survival | N=30 | longer survival | N=615 |
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=18 | older | N=3 | younger | N=15 |
PRIMARY SITE OF DISEASE | Kruskal-Wallis test | N=261 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=2 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=10 | higher stage | N=1 | lower stage | N=9 |
PATHOLOGY N STAGE | Spearman correlation test | N=7 | higher stage | N=2 | lower stage | N=5 |
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
MELANOMA ULCERATION | Wilcoxon test | N=0 | ||||
MELANOMA PRIMARY KNOWN | Wilcoxon test | N=0 | ||||
BRESLOW THICKNESS | Spearman correlation test | N=73 | higher breslow.thickness | N=19 | lower breslow.thickness | N=54 |
GENDER | Wilcoxon test | N=5 | male | N=5 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
645 genes 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) | 0-124.3 (median=14.1) |
censored | N = 138 | |
death | N = 134 | |
Significant markers | N = 645 | |
associated with shorter survival | 30 | |
associated with longer survival | 615 |
Table S2. Get Full Table List of top 10 genes significantly associated with 'Time from Specimen Diagnosis to Death' by Cox regression test
HazardRatio | Wald_P | Q | C_index | |
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SAMSN1|64092 | 0.76 | 4.238e-12 | 7.7e-08 | 0.321 |
CXCL10|3627 | 0.8 | 1.259e-11 | 2.3e-07 | 0.313 |
EAF2|55840 | 0.65 | 1.302e-11 | 2.4e-07 | 0.322 |
GBP5|115362 | 0.81 | 2.59e-11 | 4.7e-07 | 0.324 |
LAG3|3902 | 0.79 | 2.944e-11 | 5.3e-07 | 0.325 |
CD38|952 | 0.81 | 3.099e-11 | 5.6e-07 | 0.324 |
GCH1|2643 | 0.67 | 4.601e-11 | 8.3e-07 | 0.321 |
CD80|941 | 0.75 | 5.248e-11 | 9.5e-07 | 0.321 |
GBP2|2634 | 0.72 | 7.245e-11 | 1.3e-06 | 0.328 |
B2M|567 | 0.64 | 1.097e-10 | 2e-06 | 0.329 |
Table S3. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.2-357.4 (median=47.5) |
censored | N = 144 | |
death | N = 135 | |
Significant markers | N = 0 |
Table S4. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 55.74 (15) |
Significant markers | N = 18 | |
pos. correlated | 3 | |
neg. correlated | 15 |
Table S5. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
ACOX2|8309 | -0.3363 | 7.849e-09 | 0.000142 |
CMBL|134147 | -0.2956 | 4.719e-07 | 0.00853 |
FAM84B|157638 | -0.2947 | 5.148e-07 | 0.00931 |
MAOB|4129 | -0.2938 | 5.567e-07 | 0.0101 |
MGST2|4258 | -0.2802 | 1.91e-06 | 0.0345 |
PRDX6|9588 | -0.2778 | 2.354e-06 | 0.0426 |
PPP1R1B|84152 | -0.2865 | 3.637e-06 | 0.0658 |
PHKA1|5255 | -0.2694 | 4.817e-06 | 0.0871 |
CLEC1A|51267 | -0.2656 | 6.596e-06 | 0.119 |
MCHR1|2847 | -0.2673 | 6.982e-06 | 0.126 |
Table S6. Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'
PRIMARY.SITE.OF.DISEASE | Labels | N |
DISTANT METASTASIS | 39 | |
PRIMARY TUMOR | 4 | |
REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE | 61 | |
REGIONAL LYMPH NODE | 180 | |
Significant markers | N = 261 |
Table S7. Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'
ANOVA_P | Q | |
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C7|730 | 3.75e-11 | 6.78e-07 |
SHISA3|152573 | 1.093e-10 | 1.98e-06 |
RBP5|83758 | 1.305e-10 | 2.36e-06 |
FOXF1|2294 | 1.389e-10 | 2.51e-06 |
TMEM156|80008 | 1.746e-09 | 3.16e-05 |
C13ORF30|144809 | 2.098e-09 | 3.79e-05 |
POU2AF1|5450 | 4.266e-09 | 7.71e-05 |
CXCR5|643 | 4.638e-09 | 8.39e-05 |
MS4A1|931 | 5.536e-09 | 1e-04 |
CR2|1380 | 8.358e-09 | 0.000151 |
Table S8. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
I OR II NOS | 10 | |
STAGE 0 | 6 | |
STAGE I | 23 | |
STAGE IA | 10 | |
STAGE IB | 25 | |
STAGE II | 17 | |
STAGE IIA | 10 | |
STAGE IIB | 14 | |
STAGE IIC | 10 | |
STAGE III | 32 | |
STAGE IIIA | 14 | |
STAGE IIIB | 24 | |
STAGE IIIC | 49 | |
STAGE IV | 12 | |
Significant markers | N = 2 |
Table S9. Get Full Table List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'
ANOVA_P | Q | |
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RAI14|26064 | 1.376e-06 | 0.0249 |
SEMA3E|9723 | 8.937e-06 | 0.162 |
Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 2.43 (1.3) |
N | ||
0 | 22 | |
1 | 31 | |
2 | 60 | |
3 | 57 | |
4 | 58 | |
Significant markers | N = 10 | |
pos. correlated | 1 | |
neg. correlated | 9 |
Table S11. Get Full Table List of 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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INHA|3623 | -0.2989 | 5.287e-06 | 0.0956 |
TNFSF13B|10673 | -0.295 | 5.852e-06 | 0.106 |
GBP4|115361 | -0.2936 | 6.53e-06 | 0.118 |
LOXL4|84171 | -0.2901 | 8.463e-06 | 0.153 |
ANKRD22|118932 | -0.2901 | 8.867e-06 | 0.16 |
CDK15|65061 | 0.3133 | 1.139e-05 | 0.206 |
ARHGAP25|9938 | -0.2847 | 1.263e-05 | 0.228 |
KYNU|8942 | -0.2842 | 1.313e-05 | 0.237 |
CXCL9|4283 | -0.2815 | 1.603e-05 | 0.29 |
CXCL11|6373 | -0.2816 | 1.658e-05 | 0.3 |
Table S12. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Mean (SD) | 0.88 (1.1) |
N | ||
0 | 141 | |
1 | 52 | |
2 | 34 | |
3 | 37 | |
Significant markers | N = 7 | |
pos. correlated | 2 | |
neg. correlated | 5 |
Table S13. Get Full Table List of 7 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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C12ORF62|84987 | 0.3035 | 4.998e-07 | 0.00904 |
PTPRG|5793 | -0.2853 | 2.458e-06 | 0.0444 |
IL17RD|54756 | -0.281 | 3.531e-06 | 0.0639 |
MAML3|55534 | -0.2785 | 4.337e-06 | 0.0784 |
TMEM208|29100 | 0.2694 | 9.032e-06 | 0.163 |
LGR4|55366 | -0.2672 | 1.079e-05 | 0.195 |
RNF168|165918 | -0.2649 | 1.29e-05 | 0.233 |
Table S14. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 254 | |
M1 | 4 | |
M1A | 2 | |
M1B | 2 | |
M1C | 5 | |
Significant markers | N = 0 |
Table S15. Basic characteristics of clinical feature: 'MELANOMA.ULCERATION'
MELANOMA.ULCERATION | Labels | N |
NO | 104 | |
YES | 74 | |
Significant markers | N = 0 |
Table S16. Basic characteristics of clinical feature: 'MELANOMA.PRIMARY.KNOWN'
MELANOMA.PRIMARY.KNOWN | Labels | N |
NO | 34 | |
YES | 251 | |
Significant markers | N = 0 |
Table S17. Basic characteristics of clinical feature: 'BRESLOW.THICKNESS'
BRESLOW.THICKNESS | Mean (SD) | 3.58 (4.9) |
Significant markers | N = 73 | |
pos. correlated | 19 | |
neg. correlated | 54 |
Table S18. Get Full Table List of top 10 genes significantly correlated to 'BRESLOW.THICKNESS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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TNFSF13B|10673 | -0.3662 | 5.338e-08 | 0.000965 |
GBP4|115361 | -0.3655 | 5.668e-08 | 0.00102 |
SLC7A8|23428 | 0.3539 | 1.57e-07 | 0.00284 |
ATP6V0A1|535 | 0.3495 | 2.293e-07 | 0.00415 |
FGL2|10875 | -0.3467 | 2.886e-07 | 0.00522 |
CDK15|65061 | 0.3761 | 2.907e-07 | 0.00526 |
REEP6|92840 | 0.3423 | 4.186e-07 | 0.00757 |
RETSAT|54884 | 0.3362 | 6.849e-07 | 0.0124 |
GCNT1|2650 | -0.3346 | 7.81e-07 | 0.0141 |
TRPV2|51393 | 0.3319 | 9.689e-07 | 0.0175 |
Table S19. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 110 | |
MALE | 175 | |
Significant markers | N = 5 | |
Higher in MALE | 5 | |
Higher in FEMALE | 0 |
Table S20. Get Full Table List of 5 genes differentially expressed by 'GENDER'. 26 significant gene(s) located in sex chromosomes is(are) filtered out.
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
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CYORF15A|246126 | 3382 | 8.877e-12 | 1.6e-07 | 0.9663 |
HDHD1A|8226 | 5150 | 3.949e-11 | 7.13e-07 | 0.7325 |
NCRNA00183|554203 | 5151 | 3.989e-11 | 7.21e-07 | 0.7324 |
CYORF15B|84663 | 2372 | 5.846e-09 | 0.000106 | 0.9682 |
CA5BP|340591 | 6502 | 4.028e-06 | 0.0727 | 0.6622 |
Table S21. 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.uncv2.mRNAseq_RSEM_normalized_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 genes = 18086
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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.