(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 18295 genes and 8 clinical features across 480 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.
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2315 genes correlated to 'Time to Death'.
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ANKRD56|345079 , B3GNTL1|146712 , COL7A1|1294 , DONSON|29980 , ADAMTS14|140766 , ...
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19 genes correlated to 'AGE'.
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RANBP17|64901 , RFPL1S|10740 , WFDC1|58189 , UTY|7404 , PALLD|23022 , ...
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216 genes correlated to 'GENDER'.
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XIST|7503 , PRKY|5616 , NLGN4Y|22829 , RPS4Y1|6192 , TSIX|9383 , ...
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2625 genes correlated to 'PATHOLOGY.T'.
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NR3C2|4306 , FKBP11|51303 , TMEM150C|441027 , FAM122A|116224 , PLEKHA9|51054 , ...
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5 genes correlated to 'PATHOLOGY.N'.
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C11ORF34|349633 , PITX2|5308 , ATP6V1D|51382 , HEMGN|55363 , TMEM104|54868
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317 genes correlated to 'PATHOLOGICSPREAD(M)'.
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GARNL3|84253 , IL20RB|53833 , PLEKHA9|51054 , C22ORF9|23313 , BIRC5|332 , ...
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3057 genes correlated to 'TUMOR.STAGE'.
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PLEKHA9|51054 , NR3C2|4306 , FKBP11|51303 , FAM122A|116224 , NOP2|4839 , ...
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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=2315 | shorter survival | N=1496 | longer survival | N=819 |
AGE | Spearman correlation test | N=19 | older | N=3 | younger | N=16 |
GENDER | t test | N=216 | male | N=134 | female | N=82 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
PATHOLOGY T | Spearman correlation test | N=2625 | higher pT | N=1420 | lower pT | N=1205 |
PATHOLOGY N | t test | N=5 | n1 | N=2 | n0 | N=3 |
PATHOLOGICSPREAD(M) | t test | N=317 | m1 | N=264 | m0 | N=53 |
TUMOR STAGE | Spearman correlation test | N=3057 | higher stage | N=1674 | lower stage | N=1383 |
Time to Death | Duration (Months) | 0.1-111 (median=34.3) |
censored | N = 323 | |
death | N = 154 | |
Significant markers | N = 2315 | |
associated with shorter survival | 1496 | |
associated with longer survival | 819 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
ANKRD56|345079 | 0.71 | 0 | 0 | 0.319 |
B3GNTL1|146712 | 2.4 | 0 | 0 | 0.684 |
COL7A1|1294 | 1.32 | 0 | 0 | 0.676 |
DONSON|29980 | 2.7 | 0 | 0 | 0.686 |
ADAMTS14|140766 | 1.44 | 1.11e-16 | 2e-12 | 0.684 |
SLC16A12|387700 | 0.78 | 1.11e-16 | 2e-12 | 0.311 |
NUMBL|9253 | 1.85 | 2.22e-16 | 4.1e-12 | 0.687 |
ANAPC7|51434 | 5.8 | 3.331e-16 | 6.1e-12 | 0.677 |
STX1A|6804 | 1.73 | 3.331e-16 | 6.1e-12 | 0.678 |
RGS17|26575 | 1.43 | 4.441e-16 | 8.1e-12 | 0.666 |
AGE | Mean (SD) | 60.58 (12) |
Significant markers | N = 19 | |
pos. correlated | 3 | |
neg. correlated | 16 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
RANBP17|64901 | -0.2556 | 1.392e-08 | 0.000255 |
RFPL1S|10740 | -0.2559 | 1.702e-08 | 0.000311 |
WFDC1|58189 | -0.2476 | 3.998e-08 | 0.000731 |
UTY|7404 | -0.2758 | 1.044e-07 | 0.00191 |
PALLD|23022 | -0.2349 | 1.983e-07 | 0.00363 |
NEFH|4744 | -0.2324 | 2.701e-07 | 0.00494 |
DIO2|1734 | -0.2285 | 4.416e-07 | 0.00808 |
FNDC1|84624 | -0.2249 | 6.595e-07 | 0.0121 |
ZNF610|162963 | -0.2249 | 6.608e-07 | 0.0121 |
KDM5D|8284 | -0.248 | 8.594e-07 | 0.0157 |
GENDER | Labels | N |
FEMALE | 167 | |
MALE | 313 | |
Significant markers | N = 216 | |
Higher in MALE | 134 | |
Higher in FEMALE | 82 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503 | -43.08 | 3.603e-160 | 6.59e-156 | 0.982 |
PRKY|5616 | 37.98 | 1.52e-104 | 2.78e-100 | 0.9797 |
NLGN4Y|22829 | 34.69 | 2.124e-76 | 3.89e-72 | 0.9752 |
RPS4Y1|6192 | 35.02 | 2.133e-71 | 3.9e-67 | 0.9859 |
TSIX|9383 | -23.71 | 3.977e-69 | 7.27e-65 | 0.9659 |
ZFY|7544 | 34.73 | 1.837e-65 | 3.36e-61 | 0.9783 |
DDX3Y|8653 | 30.27 | 1.611e-56 | 2.95e-52 | 0.9739 |
KDM5C|8242 | -16.81 | 1.069e-48 | 1.96e-44 | 0.8949 |
NCRNA00183|554203 | -16.02 | 1.752e-43 | 3.2e-39 | 0.8608 |
KDM5D|8284 | 24.55 | 1.134e-38 | 2.07e-34 | 0.9708 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 90.88 (18) |
Score | N | |
0 | 1 | |
70 | 1 | |
80 | 3 | |
90 | 12 | |
100 | 17 | |
Significant markers | N = 0 |
PATHOLOGY.T | Mean (SD) | 1.91 (0.97) |
N | ||
T1 | 238 | |
T2 | 60 | |
T3 | 171 | |
T4 | 11 | |
Significant markers | N = 2625 | |
pos. correlated | 1420 | |
neg. correlated | 1205 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NR3C2|4306 | -0.4024 | 4.14e-20 | 7.57e-16 |
FKBP11|51303 | 0.3887 | 9.19e-19 | 1.68e-14 |
TMEM150C|441027 | -0.3833 | 3.014e-18 | 5.51e-14 |
FAM122A|116224 | -0.3831 | 3.156e-18 | 5.77e-14 |
PLEKHA9|51054 | 0.3798 | 6.4e-18 | 1.17e-13 |
ZNF132|7691 | -0.3759 | 1.465e-17 | 2.68e-13 |
ACADSB|36 | -0.3725 | 3.046e-17 | 5.57e-13 |
PTPRB|5787 | -0.372 | 3.375e-17 | 6.17e-13 |
FAM160A1|729830 | -0.3714 | 3.816e-17 | 6.98e-13 |
ANKRD56|345079 | -0.3711 | 4.375e-17 | 8e-13 |
PATHOLOGY.N | Labels | N |
N0 | 228 | |
N1 | 17 | |
Significant markers | N = 5 | |
Higher in N1 | 2 | |
Higher in N0 | 3 |
T(pos if higher in 'N1') | ttestP | Q | AUC | |
---|---|---|---|---|
C11ORF34|349633 | -7.72 | 5.065e-09 | 9.26e-05 | 0.719 |
PITX2|5308 | 6.94 | 1.839e-07 | 0.00336 | 0.785 |
ATP6V1D|51382 | -6.13 | 4.006e-07 | 0.00732 | 0.7495 |
HEMGN|55363 | -5.93 | 8.15e-07 | 0.0149 | 0.7437 |
TMEM104|54868 | 5.94 | 2.491e-06 | 0.0455 | 0.8055 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 403 | |
M1 | 77 | |
Significant markers | N = 317 | |
Higher in M1 | 264 | |
Higher in M0 | 53 |
T(pos if higher in 'M1') | ttestP | Q | AUC | |
---|---|---|---|---|
GARNL3|84253 | -6.98 | 2.078e-10 | 3.8e-06 | 0.7458 |
IL20RB|53833 | 6.7 | 1.089e-09 | 1.99e-05 | 0.7308 |
PLEKHA9|51054 | 6.68 | 1.135e-09 | 2.08e-05 | 0.7383 |
C22ORF9|23313 | 6.61 | 1.462e-09 | 2.67e-05 | 0.735 |
BIRC5|332 | 6.63 | 1.615e-09 | 2.95e-05 | 0.7295 |
INHBE|83729 | 6.55 | 2.516e-09 | 4.6e-05 | 0.7275 |
NFE2L3|9603 | 6.48 | 2.544e-09 | 4.65e-05 | 0.7237 |
TYMP|1890 | 6.38 | 3.096e-09 | 5.66e-05 | 0.7102 |
OIP5|11339 | 6.38 | 4.433e-09 | 8.11e-05 | 0.7251 |
CENPA|1058 | 6.35 | 6.395e-09 | 0.000117 | 0.7237 |
TUMOR.STAGE | Mean (SD) | 2.09 (1.2) |
N | ||
Stage 1 | 234 | |
Stage 2 | 48 | |
Stage 3 | 117 | |
Stage 4 | 81 | |
Significant markers | N = 3057 | |
pos. correlated | 1674 | |
neg. correlated | 1383 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
PLEKHA9|51054 | 0.4116 | 4.754e-21 | 8.7e-17 |
NR3C2|4306 | -0.4073 | 1.329e-20 | 2.43e-16 |
FKBP11|51303 | 0.4063 | 1.655e-20 | 3.03e-16 |
FAM122A|116224 | -0.3988 | 9.48e-20 | 1.73e-15 |
NOP2|4839 | 0.3897 | 7.358e-19 | 1.35e-14 |
TSPAN7|7102 | -0.3858 | 1.741e-18 | 3.18e-14 |
ALDH6A1|4329 | -0.385 | 2.071e-18 | 3.79e-14 |
ACADSB|36 | -0.382 | 4.016e-18 | 7.34e-14 |
PTPRB|5787 | -0.3796 | 6.725e-18 | 1.23e-13 |
FAM160A1|729830 | -0.379 | 7.664e-18 | 1.4e-13 |
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Expresson data file = KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = KIRC-TP.clin.merged.picked.txt
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Number of patients = 480
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Number of genes = 18295
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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 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.