(primary solid tumor cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18308 genes and 6 clinical features across 110 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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100 genes correlated to 'Time to Death'.
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PGAM1|5223 , CBARA1|10367 , CCNY|219771 , PPA1|5464 , CUEDC2|79004 , ...
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13 genes correlated to 'AGE'.
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TRMT2B|79979 , SAR1A|56681 , NBL1|4681 , CCNY|219771 , CDC123|8872 , ...
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23 genes correlated to 'GENDER'.
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XIST|7503 , ZFY|7544 , PRKY|5616 , RPS4Y1|6192 , KDM5D|8284 , ...
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1138 genes correlated to 'HISTOLOGICAL.TYPE'.
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AK2|204 , LRRC42|115353 , TXNDC12|51060 , ZNF691|51058 , TMEM69|51249 , ...
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31 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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C9ORF93|203238 , LMBRD2|92255 , SLC25A46|91137 , ZDHHC21|340481 , POLR2J|5439 , ...
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No genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'
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=100 | shorter survival | N=24 | longer survival | N=76 |
AGE | Spearman correlation test | N=13 | older | N=1 | younger | N=12 |
GENDER | t test | N=23 | male | N=15 | female | N=8 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=1138 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=31 | yes | N=20 | no | N=11 |
Time to Death | Duration (Months) | 0-211.2 (median=19) |
censored | N = 69 | |
death | N = 41 | |
Significant markers | N = 100 | |
associated with shorter survival | 24 | |
associated with longer survival | 76 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
PGAM1|5223 | 0.15 | 6.68e-09 | 0.00012 | 0.214 |
CBARA1|10367 | 0.12 | 7.695e-09 | 0.00014 | 0.257 |
CCNY|219771 | 0.07 | 1e-08 | 0.00018 | 0.226 |
PPA1|5464 | 0.14 | 1.253e-08 | 0.00023 | 0.25 |
CUEDC2|79004 | 0.08 | 1.67e-08 | 0.00031 | 0.261 |
ZRANB1|54764 | 0.13 | 1.819e-08 | 0.00033 | 0.223 |
CGREF1|10669 | 0.4 | 2.253e-08 | 0.00041 | 0.308 |
ARL3|403 | 0.15 | 2.536e-08 | 0.00046 | 0.209 |
SLITRK5|26050 | 0.33 | 2.869e-08 | 0.00052 | 0.284 |
LOC254559|254559 | 0.5 | 3.272e-08 | 6e-04 | 0.283 |
AGE | Mean (SD) | 42.95 (13) |
Significant markers | N = 13 | |
pos. correlated | 1 | |
neg. correlated | 12 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
TRMT2B|79979 | 0.4893 | 5.819e-08 | 0.00107 |
SAR1A|56681 | -0.4886 | 6.138e-08 | 0.00112 |
NBL1|4681 | -0.4805 | 1.079e-07 | 0.00198 |
CCNY|219771 | -0.4796 | 1.149e-07 | 0.0021 |
CDC123|8872 | -0.4768 | 1.393e-07 | 0.00255 |
RBM17|84991 | -0.4692 | 2.339e-07 | 0.00428 |
DTX4|23220 | -0.4663 | 2.834e-07 | 0.00519 |
MKX|283078 | -0.4592 | 4.509e-07 | 0.00825 |
LOC100128292|100128292 | -0.4565 | 5.363e-07 | 0.00981 |
OTUD1|220213 | -0.4491 | 8.621e-07 | 0.0158 |
GENDER | Labels | N |
FEMALE | 50 | |
MALE | 60 | |
Significant markers | N = 23 | |
Higher in MALE | 15 | |
Higher in FEMALE | 8 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503 | -39.21 | 5.231e-63 | 9.57e-59 | 1 |
ZFY|7544 | 47.2 | 2.525e-59 | 4.62e-55 | 1 |
PRKY|5616 | 25.31 | 2.249e-43 | 4.12e-39 | 0.9996 |
RPS4Y1|6192 | 38.96 | 4.013e-42 | 7.34e-38 | 1 |
KDM5D|8284 | 52.17 | 6.693e-39 | 1.22e-34 | 1 |
NLGN4Y|22829 | 24.17 | 1.097e-37 | 2.01e-33 | 0.9966 |
TSIX|9383 | -20.98 | 9.775e-37 | 1.79e-32 | 1 |
USP9Y|8287 | 45.68 | 8.53e-33 | 1.56e-28 | 1 |
DDX3Y|8653 | 46.36 | 4.11e-32 | 7.52e-28 | 1 |
EIF1AY|9086 | 44.86 | 4.043e-19 | 7.4e-15 | 1 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 88.62 (11) |
Score | N | |
50 | 2 | |
70 | 3 | |
80 | 10 | |
90 | 27 | |
100 | 16 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ASTROCYTOMA | 36 | |
OLIGOASTROCYTOMA | 27 | |
OLIGODENDROGLIOMA | 46 | |
Significant markers | N = 1138 |
ANOVA_P | Q | |
---|---|---|
AK2|204 | 1.386e-15 | 2.54e-11 |
LRRC42|115353 | 4.533e-15 | 8.3e-11 |
TXNDC12|51060 | 4.792e-15 | 8.77e-11 |
ZNF691|51058 | 1.226e-14 | 2.24e-10 |
TMEM69|51249 | 2.538e-14 | 4.65e-10 |
FPGT|8790 | 5.019e-14 | 9.19e-10 |
ADPRHL2|54936 | 5.25e-14 | 9.61e-10 |
TAF12|6883 | 5.598e-14 | 1.02e-09 |
TRAPPC3|27095 | 5.733e-14 | 1.05e-09 |
CAP1|10487 | 6.023e-14 | 1.1e-09 |
31 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 66 | |
YES | 44 | |
Significant markers | N = 31 | |
Higher in YES | 20 | |
Higher in NO | 11 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
C9ORF93|203238 | 5.95 | 3.383e-08 | 0.000619 | 0.8034 |
LMBRD2|92255 | 5.89 | 4.679e-08 | 0.000857 | 0.7837 |
SLC25A46|91137 | 5.64 | 1.444e-07 | 0.00264 | 0.7738 |
ZDHHC21|340481 | 5.59 | 1.753e-07 | 0.00321 | 0.7855 |
POLR2J|5439 | -5.61 | 1.786e-07 | 0.00327 | 0.7724 |
TTBK2|146057 | 5.54 | 2.397e-07 | 0.00439 | 0.7824 |
ZNHIT1|10467 | -5.46 | 3.39e-07 | 0.0062 | 0.77 |
ADAM22|53616 | 5.43 | 3.525e-07 | 0.00645 | 0.7769 |
PTPN4|5775 | 5.37 | 4.716e-07 | 0.00863 | 0.7603 |
MYCBP2|23077 | 5.3 | 6.736e-07 | 0.0123 | 0.7534 |
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Expresson data file = LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = LGG-TP.clin.merged.picked.txt
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Number of patients = 110
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Number of genes = 18308
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Number of clinical features = 6
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.