This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18327 genes and 8 clinical features across 229 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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11 genes correlated to 'Time to Death'.
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CYB5B|80777 , FGD3|89846 , TXNDC9|10190 , ODF3B|440836 , SLC25A45|283130 , ...
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24 genes correlated to 'GENDER'.
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XIST|7503 , PRKY|5616 , ZFY|7544 , RPS4Y1|6192 , TSIX|9383 , ...
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3 genes correlated to 'PATHOLOGY.T'.
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SAMD8|142891 , LRRC8A|56262 , USP32|84669
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1 gene correlated to 'TUMOR.STAGE'.
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SAMD8|142891
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1 gene correlated to 'NEOADJUVANT.THERAPY'.
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NBPF14|25832
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No genes correlated to 'AGE', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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=11 | shorter survival | N=4 | longer survival | N=7 |
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=24 | male | N=9 | female | N=15 |
PATHOLOGY T | Spearman correlation test | N=3 | higher pT | N=3 | lower pT | N=0 |
PATHOLOGY N | Spearman correlation test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=1 | higher stage | N=1 | lower stage | N=0 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
NEOADJUVANT THERAPY | t test | N=1 | yes | N=0 | no | N=1 |
Time to Death | Duration (Months) | 0.1-210.9 (median=14.2) |
censored | N = 132 | |
death | N = 96 | |
Significant markers | N = 11 | |
associated with shorter survival | 4 | |
associated with longer survival | 7 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
CYB5B|80777 | 2.6 | 3.411e-08 | 0.00063 | 0.647 |
FGD3|89846 | 0.63 | 1.075e-07 | 0.002 | 0.34 |
TXNDC9|10190 | 2.2 | 9.283e-07 | 0.017 | 0.612 |
ODF3B|440836 | 0.55 | 1.653e-06 | 0.03 | 0.37 |
SLC25A45|283130 | 0.58 | 1.661e-06 | 0.03 | 0.347 |
TMED2|10959 | 2.4 | 1.982e-06 | 0.036 | 0.663 |
TOMM34|10953 | 2.3 | 2.219e-06 | 0.041 | 0.64 |
ZNF266|10781 | 0.43 | 2.339e-06 | 0.043 | 0.354 |
ZNF541|84215 | 0.79 | 2.556e-06 | 0.047 | 0.319 |
REC8|9985 | 0.73 | 2.661e-06 | 0.049 | 0.371 |
AGE | Mean (SD) | 61.14 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 59 | |
MALE | 170 | |
Significant markers | N = 24 | |
Higher in MALE | 9 | |
Higher in FEMALE | 15 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503 | -31.56 | 6.652e-58 | 1.22e-53 | 0.9896 |
PRKY|5616 | 19.55 | 1.722e-38 | 3.15e-34 | 0.9741 |
ZFY|7544 | 24.07 | 2.762e-32 | 5.06e-28 | 0.9834 |
RPS4Y1|6192 | 22.54 | 4.585e-26 | 8.4e-22 | 0.9837 |
TSIX|9383 | -13.99 | 1.465e-25 | 2.68e-21 | 0.9639 |
NLGN4Y|22829 | 17.69 | 4.072e-23 | 7.46e-19 | 0.974 |
DDX3Y|8653 | 19.35 | 6.966e-20 | 1.28e-15 | 0.9733 |
UTY|7404 | 14.45 | 1.16e-13 | 2.13e-09 | 0.9675 |
HDHD1A|8226 | -8.24 | 3.306e-13 | 6.06e-09 | 0.8239 |
USP9Y|8287 | 13.88 | 5.006e-13 | 9.17e-09 | 0.9658 |
PATHOLOGY.T | Mean (SD) | 3.02 (0.97) |
N | ||
T1 | 12 | |
T2 | 55 | |
T3 | 47 | |
T4 | 82 | |
Significant markers | N = 3 | |
pos. correlated | 3 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SAMD8|142891 | 0.3574 | 2.711e-07 | 0.00497 |
LRRC8A|56262 | 0.3444 | 7.729e-07 | 0.0142 |
USP32|84669 | 0.3335 | 1.778e-06 | 0.0326 |
PATHOLOGY.N | Mean (SD) | 1.05 (0.96) |
N | ||
N0 | 73 | |
N1 | 23 | |
N2 | 76 | |
N3 | 3 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 3.36 (0.93) |
N | ||
Stage 1 | 9 | |
Stage 2 | 34 | |
Stage 3 | 29 | |
Stage 4 | 121 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SAMD8|142891 | 0.3415 | 1.172e-06 | 0.0215 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 62 | |
YES | 167 | |
Significant markers | N = 0 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 38 | |
YES | 191 | |
Significant markers | N = 1 | |
Higher in YES | 0 | |
Higher in NO | 1 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
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NBPF14|25832 | -5.21 | 1.663e-06 | 0.0305 | 0.7224 |
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Expresson data file = HNSC.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = HNSC.clin.merged.picked.txt
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Number of patients = 229
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Number of genes = 18327
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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.