This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.
Testing the association between 2 variables and 18 clinical features across 398 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 clinical features related to at least one variables.
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2 variables correlated to 'Time to Death'.
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MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
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2 variables correlated to 'AGE'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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2 variables correlated to 'AGE_mutation.rate'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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2 variables correlated to 'NEOPLASM.DISEASESTAGE'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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2 variables correlated to 'PATHOLOGY.T.STAGE'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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1 variable correlated to 'HISTOLOGICAL.TYPE'.
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MUTATIONRATE_SILENT
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2 variables correlated to 'EXTRATHYROIDAL.EXTENSION'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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2 variables correlated to 'COMPLETENESS.OF.RESECTION'.
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MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT
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1 variable correlated to 'TUMOR.SIZE'.
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MUTATIONRATE_NONSYNONYMOUS
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1 variable correlated to 'RACE'.
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MUTATIONRATE_NONSYNONYMOUS
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No variables correlated to 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'GENDER', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'RADIATIONEXPOSURE', 'NUMBER.OF.LYMPH.NODES', 'MULTIFOCALITY', and 'ETHNICITY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant variables | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=2 | shorter survival | N=2 | longer survival | N=0 |
AGE | Spearman correlation test | N=2 | older | N=2 | younger | N=0 |
AGE | Linear Regression Analysis | N=2 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=2 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=2 | higher stage | N=2 | lower stage | N=0 |
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
GENDER | Wilcoxon test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=1 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
RADIATIONEXPOSURE | Wilcoxon test | N=0 | ||||
EXTRATHYROIDAL EXTENSION | Kruskal-Wallis test | N=2 | ||||
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=2 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
MULTIFOCALITY | Wilcoxon test | N=0 | ||||
TUMOR SIZE | Spearman correlation test | N=1 | higher tumor.size | N=1 | lower tumor.size | N=0 |
RACE | Kruskal-Wallis test | N=1 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0-158.8 (median=17) |
censored | N = 383 | |
death | N = 13 | |
Significant variables | N = 2 | |
associated with shorter survival | 2 | |
associated with longer survival | 0 |
AGE | Mean (SD) | 47.07 (16) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
AGE | Mean (SD) | 47.07 (16) |
Significant variables | N = 2 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 228 | |
STAGE II | 44 | |
STAGE III | 83 | |
STAGE IV | 2 | |
STAGE IVA | 33 | |
STAGE IVC | 6 | |
Significant variables | N = 2 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.1 (0.87) |
N | ||
1 | 116 | |
2 | 137 | |
3 | 127 | |
4 | 15 | |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 188 | |
class1 | 169 | |
Significant variables | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 219 | |
M1 | 7 | |
MX | 171 | |
Significant variables | N = 0 |
GENDER | Labels | N |
FEMALE | 297 | |
MALE | 101 | |
Significant variables | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
OTHER SPECIFY | 6 | |
THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | 280 | |
THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | 83 | |
THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) | 29 | |
Significant variables | N = 1 |
ANOVA_P | Q | |
---|---|---|
MUTATIONRATE_SILENT | 0.04024 | 0.0805 |
No variable related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 12 | |
YES | 386 | |
Significant variables | N = 0 |
RADIATIONEXPOSURE | Labels | N |
NO | 334 | |
YES | 15 | |
Significant variables | N = 0 |
2 variables related to 'EXTRATHYROIDAL.EXTENSION'.
EXTRATHYROIDAL.EXTENSION | Labels | N |
MINIMAL (T3) | 102 | |
MODERATE/ADVANCED (T4A) | 11 | |
NONE | 270 | |
VERY ADVANCED (T4B) | 1 | |
Significant variables | N = 2 |
2 variables related to 'COMPLETENESS.OF.RESECTION'.
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 311 | |
R1 | 37 | |
R2 | 3 | |
RX | 22 | |
Significant variables | N = 2 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 3.3 (6) |
Significant variables | N = 0 |
MULTIFOCALITY | Labels | N |
MULTIFOCAL | 180 | |
UNIFOCAL | 209 | |
Significant variables | N = 0 |
TUMOR.SIZE | Mean (SD) | 2.97 (1.6) |
Significant variables | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MUTATIONRATE_NONSYNONYMOUS | 0.134 | 0.01577 | 0.0315 |
RACE | Labels | N |
ASIAN | 35 | |
BLACK OR AFRICAN AMERICAN | 18 | |
WHITE | 258 | |
Significant variables | N = 1 |
ANOVA_P | Q | |
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MUTATIONRATE_NONSYNONYMOUS | 0.04774 | 0.0955 |
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Expresson data file = THCA-TP.patients.counts_and_rates.txt
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Clinical data file = THCA-TP.merged_data.txt
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Number of patients = 398
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Number of variables = 2
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Number of clinical features = 18
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.