This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 12042 genes and 8 clinical features across 525 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 6 clinical features related to at least one genes.
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155 genes correlated to 'AGE'.
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FBXO17 , KIAA0495 , RANBP17 , NOL3 , TUSC3 , ...
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9 genes correlated to 'GENDER'.
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JARID1D , CYORF15B , HDHD1A , UTX , JARID1C , ...
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3 genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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TM4SF20 , ZBP1 , WRNIP1
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119 genes correlated to 'HISTOLOGICAL.TYPE'.
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PDIA6 , NPM1 , HNRPF , ALDH18A1 , NPM3 , ...
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9 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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STAG2 , RPL13 , SLC37A4 , CTPS2 , SH3TC2 , ...
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2 genes correlated to 'RACE'.
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CRYBB2 , PSPH
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No genes correlated to 'Time to Death', 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=155 | older | N=133 | younger | N=22 |
GENDER | Wilcoxon test | N=9 | male | N=9 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=3 | higher score | N=3 | lower score | N=0 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=119 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=9 | yes | N=9 | no | N=0 |
RACE | Kruskal-Wallis test | N=2 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0.1-127.6 (median=10.4) |
censored | N = 80 | |
death | N = 445 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 57.68 (15) |
Significant markers | N = 155 | |
pos. correlated | 133 | |
neg. correlated | 22 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
FBXO17 | 0.3074 | 5.924e-13 | 7.13e-09 |
KIAA0495 | 0.2949 | 5.437e-12 | 6.55e-08 |
RANBP17 | -0.2916 | 9.501e-12 | 1.14e-07 |
NOL3 | 0.2831 | 3.903e-11 | 4.7e-07 |
TUSC3 | -0.2761 | 1.217e-10 | 1.46e-06 |
C14ORF45 | 0.2726 | 2.115e-10 | 2.55e-06 |
DRG2 | 0.2617 | 1.147e-09 | 1.38e-05 |
C5ORF21 | 0.2498 | 6.579e-09 | 7.92e-05 |
CBR1 | 0.2455 | 1.203e-08 | 0.000145 |
H2AFY2 | -0.2455 | 1.206e-08 | 0.000145 |
GENDER | Labels | N |
FEMALE | 205 | |
MALE | 320 | |
Significant markers | N = 9 | |
Higher in MALE | 9 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
JARID1D | 62786 | 5.665e-70 | 6.82e-66 | 0.9571 |
CYORF15B | 61883 | 6.228e-66 | 7.5e-62 | 0.9433 |
HDHD1A | 15478 | 1.702e-24 | 2.05e-20 | 0.7641 |
UTX | 20401 | 2.639e-13 | 3.17e-09 | 0.689 |
JARID1C | 20621 | 6.875e-13 | 8.27e-09 | 0.6857 |
CXORF15 | 24198 | 3.927e-07 | 0.00472 | 0.6311 |
GPR88 | 41229 | 6.68e-07 | 0.00803 | 0.6285 |
RCAN2 | 40921 | 1.678e-06 | 0.0202 | 0.6238 |
ADAM20 | 25476 | 1.569e-05 | 0.189 | 0.6116 |
3 genes related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 77.22 (14) |
Significant markers | N = 3 | |
pos. correlated | 3 | |
neg. correlated | 0 |
HISTOLOGICAL.TYPE | Labels | N |
GLIOBLASTOMA MULTIFORME (GBM) | 6 | |
TREATED PRIMARY GBM | 20 | |
UNTREATED PRIMARY (DE NOVO) GBM | 499 | |
Significant markers | N = 119 |
9 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 359 | |
YES | 166 | |
Significant markers | N = 9 | |
Higher in YES | 9 | |
Higher in NO | 0 |
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
STAG2 | 22266 | 3.173e-06 | 0.0382 | 0.6264 |
RPL13 | 22288 | 3.39e-06 | 0.0408 | 0.626 |
SLC37A4 | 22542 | 7.172e-06 | 0.0863 | 0.6217 |
CTPS2 | 22598 | 8.433e-06 | 0.102 | 0.6208 |
SH3TC2 | 36852 | 1.272e-05 | 0.153 | 0.6184 |
H1F0 | 22762 | 1.346e-05 | 0.162 | 0.618 |
STT3A | 22839 | 1.672e-05 | 0.201 | 0.6168 |
MAP7D3 | 22854 | 1.743e-05 | 0.21 | 0.6165 |
NUTF2 | 22865 | 1.797e-05 | 0.216 | 0.6163 |
RACE | Labels | N |
ASIAN | 13 | |
BLACK OR AFRICAN AMERICAN | 31 | |
WHITE | 462 | |
Significant markers | N = 2 |
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Expresson data file = GBM-TP.medianexp.txt
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Clinical data file = GBM-TP.merged_data.txt
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Number of patients = 525
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Number of genes = 12042
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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 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.