This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17843 genes and 5 clinical features across 25 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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4 genes correlated to 'GENDER'.
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DDX3Y|8653 , XIST|7503 , RPS4Y1|6192 , ZFY|7544
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15 genes correlated to 'LYMPH.NODE.METASTASIS'.
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WDR20|91833 , GRIP1|23426 , C14ORF159|80017 , GLRX5|51218 , C14ORF109|26175 , ...
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No genes correlated to 'AGE', 'DISTANT.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.
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=4 | male | N=3 | female | N=1 |
DISTANT METASTASIS | ANOVA test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=15 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=0 |
AGE | Mean (SD) | 52.32 (15) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 11 | |
MALE | 14 | |
Significant markers | N = 4 | |
Higher in MALE | 3 | |
Higher in FEMALE | 1 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
DDX3Y|8653 | 17.12 | 3.268e-11 | 5.78e-07 | 1 |
XIST|7503 | -13.36 | 3.034e-10 | 5.37e-06 | 1 |
RPS4Y1|6192 | 14.54 | 5.06e-09 | 8.95e-05 | 1 |
ZFY|7544 | 9.56 | 5.237e-08 | 0.000927 | 1 |
DISTANT.METASTASIS | Labels | N |
M0 | 2 | |
M1 | 2 | |
MX | 3 | |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 13 | |
N1 | 2 | |
NX | 10 | |
Significant markers | N = 15 |
ANOVA_P | Q | |
---|---|---|
WDR20|91833 | 2.75e-10 | 4.91e-06 |
GRIP1|23426 | 3.23e-08 | 0.000576 |
C14ORF159|80017 | 5.028e-08 | 0.000897 |
GLRX5|51218 | 1.081e-07 | 0.00193 |
C14ORF109|26175 | 1.425e-07 | 0.00254 |
ASAM|79827 | 2.374e-07 | 0.00423 |
UBR7|55148 | 2.808e-07 | 0.00501 |
KIAA1543|57662 | 7.539e-07 | 0.0134 |
ZNF22|7570 | 7.944e-07 | 0.0142 |
TWIST2|117581 | 8.644e-07 | 0.0154 |
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Expresson data file = KICH-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = KICH-TP.clin.merged.picked.txt
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Number of patients = 25
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Number of genes = 17843
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Number of clinical features = 5
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.