This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18305 genes and 8 clinical features across 72 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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14 genes correlated to 'GENDER'.
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XIST|7503 , RPS4Y1|6192 , DDX3Y|8653 , UTY|7404 , NLGN4Y|22829 , ...
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48 genes correlated to 'HISTOLOGICAL.TYPE'.
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EFNA5|1946 , PIPOX|51268 , AGR3|155465 , FNTB|2342 , SERPINA1|5265 , ...
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1 gene correlated to 'PATHOLOGY.N'.
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CLNK|116449
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5 genes correlated to 'PATHOLOGICSPREAD(M)'.
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TMEM84|283673 , ODZ1|10178 , CTNNA2|1496 , LOC100189589|100189589 , C1ORF114|57821
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No genes correlated to 'Time to Death', 'AGE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
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=0 | ||||
GENDER | t test | N=14 | male | N=11 | female | N=3 |
HISTOLOGICAL TYPE | t test | N=48 | rectal mucinous adenocarcinoma | N=39 | rectal adenocarcinoma | N=9 |
PATHOLOGY T | Spearman correlation test | N=0 | ||||
PATHOLOGY N | Spearman correlation test | N=1 | higher pN | N=0 | lower pN | N=1 |
PATHOLOGICSPREAD(M) | t test | N=5 | m1 | N=0 | m0 | N=5 |
TUMOR STAGE | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.9-72.1 (median=10.6) |
censored | N = 39 | |
death | N = 4 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 66.75 (10) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 33 | |
MALE | 39 | |
Significant markers | N = 14 | |
Higher in MALE | 11 | |
Higher in FEMALE | 3 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503 | -19.86 | 5.762e-27 | 1.05e-22 | 0.999 |
RPS4Y1|6192 | 15.48 | 2.795e-21 | 5.12e-17 | 0.9938 |
DDX3Y|8653 | 16.43 | 8.023e-20 | 1.47e-15 | 0.9979 |
UTY|7404 | 14.04 | 1.665e-19 | 3.05e-15 | 0.9918 |
NLGN4Y|22829 | 13.94 | 1.46e-18 | 2.67e-14 | 0.9931 |
ZFY|7544 | 10.35 | 9.875e-16 | 1.81e-11 | 0.9635 |
TSIX|9383 | -9.82 | 3.694e-14 | 6.76e-10 | 0.9293 |
EIF1AY|9086 | 11.72 | 2.638e-13 | 4.83e-09 | 0.9894 |
TTTY15|64595 | 10.08 | 7.814e-13 | 1.43e-08 | 0.9737 |
KDM5D|8284 | 12.46 | 5.451e-12 | 9.97e-08 | 0.994 |
HISTOLOGICAL.TYPE | Labels | N |
RECTAL ADENOCARCINOMA | 60 | |
RECTAL MUCINOUS ADENOCARCINOMA | 8 | |
Significant markers | N = 48 | |
Higher in RECTAL MUCINOUS ADENOCARCINOMA | 39 | |
Higher in RECTAL ADENOCARCINOMA | 9 |
T(pos if higher in 'RECTAL MUCINOUS ADENOCARCINOMA') | ttestP | Q | AUC | |
---|---|---|---|---|
EFNA5|1946 | 9.48 | 1.235e-11 | 2.24e-07 | 0.8917 |
PIPOX|51268 | -7.64 | 4.444e-10 | 8.05e-06 | 0.8312 |
AGR3|155465 | 7.82 | 3.525e-09 | 6.39e-05 | 0.8938 |
FNTB|2342 | 6.98 | 9.547e-09 | 0.000173 | 0.8479 |
SERPINA1|5265 | 8.83 | 3.275e-08 | 0.000593 | 0.9312 |
FHL2|2274 | 7.39 | 3.816e-08 | 0.000692 | 0.8958 |
B3GNT6|192134 | 9.67 | 3.818e-08 | 0.000692 | 0.9562 |
EIF2S1|1965 | 6.47 | 4.994e-08 | 0.000905 | 0.8479 |
GNPNAT1|64841 | 7.27 | 5.152e-08 | 0.000933 | 0.9229 |
SNX20|124460 | 6.83 | 5.511e-08 | 0.000998 | 0.8354 |
PATHOLOGY.T | Mean (SD) | 2.71 (0.68) |
N | ||
T1 | 5 | |
T2 | 15 | |
T3 | 48 | |
T4 | 4 | |
Significant markers | N = 0 |
PATHOLOGY.N | Mean (SD) | 0.56 (0.77) |
N | ||
N0 | 44 | |
N1 | 16 | |
N2 | 12 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
CLNK|116449 | -0.5354 | 2.552e-06 | 0.0467 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 61 | |
M1 | 11 | |
Significant markers | N = 5 | |
Higher in M1 | 0 | |
Higher in M0 | 5 |
T(pos if higher in 'M1') | ttestP | Q | AUC | |
---|---|---|---|---|
TMEM84|283673 | -7.71 | 5.132e-10 | 9.34e-06 | 0.8804 |
ODZ1|10178 | -6.43 | 4.492e-07 | 0.00818 | 0.8889 |
CTNNA2|1496 | -5.9 | 6.226e-07 | 0.0113 | 0.8661 |
LOC100189589|100189589 | -5.78 | 2.571e-06 | 0.0468 | 0.8283 |
C1ORF114|57821 | -5.69 | 2.716e-06 | 0.0494 | 0.8849 |
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Expresson data file = READ.mRNAseq_RPKM_log2.txt
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Clinical data file = READ.clin.merged.picked.txt
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Number of patients = 72
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Number of genes = 18305
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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.