This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 17994 genes and 5 clinical features across 132 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one genes.
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44 genes correlated to 'AGE'.
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NDC80|10403 , KIF4A|24137 , GTSE1|51512 , FAM83D|81610 , CDCA2|157313 , ...
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3 genes correlated to 'GENDER'.
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NCRNA00183|554203 , CYORF15A|246126 , CYORF15B|84663
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No genes correlated to 'Time to Death', 'RACE', and 'ETHNICITY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=44 | older | N=0 | younger | N=44 |
GENDER | Wilcoxon test | N=3 | male | N=3 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0.1-303.1 (median=16.9) |
censored | N = 128 | |
death | N = 4 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 48.8 (16) |
Significant markers | N = 44 | |
pos. correlated | 0 | |
neg. correlated | 44 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NDC80|10403 | -0.4871 | 3.171e-09 | 5.71e-05 |
KIF4A|24137 | -0.4643 | 2.054e-08 | 0.00037 |
GTSE1|51512 | -0.4599 | 2.899e-08 | 0.000522 |
FAM83D|81610 | -0.4586 | 3.199e-08 | 0.000576 |
CDCA2|157313 | -0.4585 | 3.232e-08 | 0.000581 |
PLK1|5347 | -0.4543 | 4.459e-08 | 0.000802 |
CCNB2|9133 | -0.4498 | 6.273e-08 | 0.00113 |
KIF20A|10112 | -0.4458 | 8.499e-08 | 0.00153 |
DIAPH3|81624 | -0.4429 | 1.172e-07 | 0.00211 |
CEP55|55165 | -0.4332 | 2.13e-07 | 0.00383 |
GENDER | Labels | N |
FEMALE | 75 | |
MALE | 57 | |
Significant markers | N = 3 | |
Higher in MALE | 3 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
NCRNA00183|554203 | 701 | 4.194e-11 | 7.54e-07 | 0.836 |
CYORF15A|246126 | 798 | 8.459e-09 | 0.000152 | 1 |
CYORF15B|84663 | 798 | 8.459e-09 | 0.000152 | 1 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 1 | |
ASIAN | 5 | |
BLACK OR AFRICAN AMERICAN | 9 | |
WHITE | 114 | |
Significant markers | N = 0 |
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Expresson data file = PCPG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = PCPG-TP.merged_data.txt
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Number of patients = 132
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Number of genes = 17994
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Number of clinical features = 5
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.
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.