This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.
Testing the association between 2 variables and 13 clinical features across 221 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one variables.
-
2 variables correlated to 'AGE'.
-
MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS
-
1 variable correlated to 'AGE_mutation.rate'.
-
MUTATIONRATE_SILENT
-
No variables correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'GENDER', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'COMPLETENESS.OF.RESECTION', 'NUMBER.OF.LYMPH.NODES', and 'RACE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant variables | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=2 | older | N=2 | younger | N=0 |
AGE | Linear Regression Analysis | N=1 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=0 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
GENDER | Wilcoxon test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
RACE | Kruskal-Wallis test | N=0 |
Time to Death | Duration (Months) | 0.1-105.1 (median=12) |
censored | N = 130 | |
death | N = 65 | |
Significant variables | N = 0 |
AGE | Mean (SD) | 66.34 (11) |
Significant variables | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
AGE | Mean (SD) | 66.34 (11) |
Significant variables | N = 1 |
Adj.R.squared | F | P | Residual.std.err | DF | coef(intercept) | coef.p(intercept) | |
---|---|---|---|---|---|---|---|
MUTATIONRATE_SILENT | 0.0145 | 4.16 | 0.0426 | 7.98e-06 | 214 | 1.01e-07 ( -2.55e-06 ) | 0.0426 ( 0.445 ) |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 1 | |
STAGE IA | 6 | |
STAGE IB | 23 | |
STAGE II | 23 | |
STAGE IIA | 21 | |
STAGE IIB | 31 | |
STAGE III | 3 | |
STAGE IIIA | 33 | |
STAGE IIIB | 24 | |
STAGE IIIC | 17 | |
STAGE IV | 24 | |
Significant variables | N = 0 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.85 (0.81) |
N | ||
1 | 7 | |
2 | 66 | |
3 | 90 | |
4 | 49 | |
Significant variables | N = 0 |
PATHOLOGY.N.STAGE | Mean (SD) | 1.22 (1.1) |
N | ||
0 | 70 | |
1 | 63 | |
2 | 35 | |
3 | 41 | |
Significant variables | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 195 | |
M1 | 16 | |
MX | 10 | |
Significant variables | N = 0 |
GENDER | Labels | N |
FEMALE | 88 | |
MALE | 133 | |
Significant variables | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
STOMACH ADENOCARCINOMA DIFFUSE TYPE | 32 | |
STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | 108 | |
STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | 34 | |
STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE | 26 | |
STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE | 1 | |
STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE | 14 | |
STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE | 4 | |
STOMACH ADENOCARCINOMA SIGNET RING TYPE | 1 | |
Significant variables | N = 0 |
No variable related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 6 | |
YES | 215 | |
Significant variables | N = 0 |
No variable related to 'COMPLETENESS.OF.RESECTION'.
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 171 | |
R1 | 7 | |
R2 | 10 | |
RX | 24 | |
Significant variables | N = 0 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 5.18 (7.5) |
Significant variables | N = 0 |
-
Expresson data file = STAD-TP.patients.counts_and_rates.txt
-
Clinical data file = STAD-TP.merged_data.txt
-
Number of patients = 221
-
Number of variables = 2
-
Number of clinical features = 13
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.