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 32 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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1 gene correlated to 'LYMPH.NODE.METASTASIS'.
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RTN4IP1
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16 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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HMGB4 , FGF21 , KCNK10 , SPAG11B , EDC3 , ...
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No genes correlated to 'Time to Death', 'AGE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'NUMBERPACKYEARSSMOKED', 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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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=0 | ||||
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
YEAROFTOBACCOSMOKINGONSET | Spearman correlation test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=1 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=16 |
Time to Death | Duration (Months) | 0.5-56.8 (median=14) |
censored | N = 27 | |
death | N = 4 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 65.7 (11) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 18 | |
MALE | 14 | |
Significant markers | N = 0 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 56.67 (49) |
Score | N | |
0 | 1 | |
80 | 1 | |
90 | 1 | |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 41.15 (15) |
Significant markers | N = 0 |
YEAROFTOBACCOSMOKINGONSET | Mean (SD) | 1968.53 (11) |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 23 | |
N1 | 4 | |
N2 | 4 | |
NX | 1 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
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RTN4IP1 | 1.542e-06 | 0.0275 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE IA | 12 | |
STAGE IB | 11 | |
STAGE IIA | 1 | |
STAGE IIB | 3 | |
STAGE IIIA | 3 | |
STAGE IV | 2 | |
Significant markers | N = 16 |
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Expresson data file = LUAD-TP.medianexp.txt
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Clinical data file = LUAD-TP.clin.merged.picked.txt
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Number of patients = 32
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Number of genes = 17814
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Number of clinical features = 8
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 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.