This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 18170 genes and 4 clinical features across 111 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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5 genes correlated to 'Time to Death'.
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MRGPRF|116535 , POU4F1|5457 , COL11A2|1302 , DMRTA2|63950 , PRKCDBP|112464
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16 genes correlated to 'GENDER'.
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NCRNA00183|554203 , HDHD1A|8226 , CYORF15A|246126 , CA5BP|340591 , CYORF15B|84663 , ...
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No genes correlated to 'AGE', and 'RACE'.
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=5 | shorter survival | N=3 | longer survival | N=2 |
AGE | Spearman correlation test | N=0 | ||||
GENDER | Wilcoxon test | N=16 | male | N=16 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 |
Time to Death | Duration (Months) | 0.1-143.4 (median=18.1) |
censored | N = 76 | |
death | N = 35 | |
Significant markers | N = 5 | |
associated with shorter survival | 3 | |
associated with longer survival | 2 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
MRGPRF|116535 | 0.66 | 1.499e-06 | 0.027 | 0.291 |
POU4F1|5457 | 1.61 | 1.636e-06 | 0.03 | 0.762 |
COL11A2|1302 | 1.41 | 2.585e-06 | 0.047 | 0.661 |
DMRTA2|63950 | 1.49 | 3.014e-06 | 0.055 | 0.712 |
PRKCDBP|112464 | 0.46 | 5.193e-06 | 0.094 | 0.253 |
AGE | Mean (SD) | 60.72 (14) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 60 | |
MALE | 51 | |
Significant markers | N = 16 | |
Higher in MALE | 16 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
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NCRNA00183|554203 | 640 | 1.414e-07 | 0.00257 | 0.7908 |
HDHD1A|8226 | 679 | 4.838e-07 | 0.00878 | 0.7781 |
CYORF15A|246126 | 510 | 7.126e-07 | 0.0129 | 1 |
CA5BP|340591 | 699 | 8.911e-07 | 0.0162 | 0.7716 |
CYORF15B|84663 | 505 | 1.171e-06 | 0.0212 | 0.9902 |
PQLC3|130814 | 2322 | 2.82e-06 | 0.0512 | 0.7588 |
GRK6|2870 | 740 | 2.987e-06 | 0.0542 | 0.7582 |
PRPSAP1|5635 | 753 | 4.333e-06 | 0.0786 | 0.7539 |
CBX1|10951 | 754 | 4.457e-06 | 0.0809 | 0.7536 |
DBF4B|80174 | 758 | 4.991e-06 | 0.0905 | 0.7523 |
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Expresson data file = SARC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = SARC-TP.merged_data.txt
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Number of patients = 111
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Number of genes = 18170
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Number of clinical features = 4
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.