This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 8 clinical features across 9 samples, statistically thresholded by Q value < 0.05, no clinical feature related to at least one genes.
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No genes correlated to 'AGE', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'NUMBERPACKYEARSSMOKED', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'YEAROFTOBACCOSMOKINGONSET'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=0 | ||||
PATHOLOGY T | t test | N=0 | ||||
PATHOLOGY N | Spearman correlation test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
TOBACCOSMOKINGHISTORYINDICATOR | ANOVA test | N=0 | ||||
YEAROFTOBACCOSMOKINGONSET | Spearman correlation test | N=0 |
AGE | Mean (SD) | 65.89 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 5 | |
MALE | 4 | |
Significant markers | N = 0 |
PATHOLOGY.T | Labels | N |
T1 | 2 | |
T2 | 7 | |
Significant markers | N = 0 |
PATHOLOGY.N | Mean (SD) | 0.78 (0.97) |
N | ||
N0 | 5 | |
N1 | 1 | |
N2 | 3 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 1.89 (1.2) |
N | ||
Stage 1 | 5 | |
Stage 2 | 1 | |
Stage 3 | 2 | |
Stage 4 | 1 | |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 46.5 (11) |
Value | N | |
30 | 1 | |
50 | 2 | |
56 | 1 | |
Significant markers | N = 0 |
No gene related to 'TOBACCOSMOKINGHISTORYINDICATOR'.
TOBACCOSMOKINGHISTORYINDICATOR | Labels | N |
CURRENT REFORMED SMOKER FOR > 15 YEARS | 2 | |
CURRENT SMOKER | 3 | |
LIFELONG NON-SMOKER | 4 | |
Significant markers | N = 0 |
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Expresson data file = MOLECULAR_NONSMOKER.medianexp.txt
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Clinical data file = MOLECULAR_NONSMOKER.clin.merged.picked.txt
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Number of patients = 9
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Number of genes = 17814
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Number of clinical features = 8
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.