This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17848 genes and 9 clinical features across 192 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
-
2 genes correlated to 'AGE'.
-
DDX27|55661 , KIAA0406|9675
-
25 genes correlated to 'GENDER'.
-
RPS4Y1|6192 , ZFY|7544 , DDX3Y|8653 , XIST|7503 , KDM5D|8284 , ...
-
101 genes correlated to 'HISTOLOGICAL.TYPE'.
-
PPP1R9A|55607 , DYNLRB1|83658 , ZIC5|85416 , MOCS3|27304 , POFUT1|23509 , ...
-
1 gene correlated to 'PATHOLOGY.N'.
-
CD2BP2|10421
-
No genes correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'NEOADJUVANT.THERAPY'.
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=2 | older | N=0 | younger | N=2 |
GENDER | t test | N=25 | male | N=13 | female | N=12 |
HISTOLOGICAL TYPE | t test | N=101 | colon mucinous adenocarcinoma | N=49 | colon adenocarcinoma | N=52 |
PATHOLOGY T | Spearman correlation test | N=0 | ||||
PATHOLOGY N | Spearman correlation test | N=1 | higher pN | N=1 | lower pN | N=0 |
PATHOLOGICSPREAD(M) | ANOVA test | N=0 | ||||
TUMOR STAGE | Spearman correlation test | N=0 | ||||
NEOADJUVANT THERAPY | t test | N=0 |
Time to Death | Duration (Months) | 0.9-71.7 (median=12.4) |
censored | N = 92 | |
death | N = 16 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 69.66 (12) |
Significant markers | N = 2 | |
pos. correlated | 0 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
DDX27|55661 | -0.3351 | 2.019e-06 | 0.036 |
KIAA0406|9675 | -0.3323 | 2.494e-06 | 0.0445 |
GENDER | Labels | N |
FEMALE | 99 | |
MALE | 93 | |
Significant markers | N = 25 | |
Higher in MALE | 13 | |
Higher in FEMALE | 12 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
RPS4Y1|6192 | 26.78 | 2.19e-63 | 3.91e-59 | 0.9974 |
ZFY|7544 | 26.95 | 7.184e-51 | 1.28e-46 | 0.9919 |
DDX3Y|8653 | 26.99 | 2.915e-47 | 5.2e-43 | 0.9951 |
XIST|7503 | -20.01 | 9.653e-40 | 1.72e-35 | 0.9806 |
KDM5D|8284 | 25.13 | 2.492e-39 | 4.45e-35 | 0.9955 |
CYORF15A|246126 | 21.19 | 7.879e-38 | 1.41e-33 | 0.9884 |
TMSB4Y|9087 | 19.26 | 1.606e-34 | 2.87e-30 | 0.975 |
PRKY|5616 | 15.19 | 2.703e-34 | 4.82e-30 | 0.9331 |
EIF1AY|9086 | 19.41 | 1.771e-28 | 3.16e-24 | 0.9901 |
NLGN4Y|22829 | 14.56 | 7.649e-28 | 1.36e-23 | 0.9474 |
HISTOLOGICAL.TYPE | Labels | N |
COLON ADENOCARCINOMA | 162 | |
COLON MUCINOUS ADENOCARCINOMA | 27 | |
Significant markers | N = 101 | |
Higher in COLON MUCINOUS ADENOCARCINOMA | 49 | |
Higher in COLON ADENOCARCINOMA | 52 |
T(pos if higher in 'COLON MUCINOUS ADENOCARCINOMA') | ttestP | Q | AUC | |
---|---|---|---|---|
PPP1R9A|55607 | 7.66 | 9.842e-12 | 1.76e-07 | 0.7523 |
DYNLRB1|83658 | -8.48 | 1.267e-11 | 2.26e-07 | 0.8425 |
ZIC5|85416 | 7.92 | 3.9e-11 | 6.96e-07 | 0.8056 |
MOCS3|27304 | -7.97 | 5.581e-11 | 9.96e-07 | 0.8185 |
POFUT1|23509 | -7.71 | 1.731e-09 | 3.09e-05 | 0.8445 |
C20ORF24|55969 | -7.34 | 1.813e-09 | 3.23e-05 | 0.8157 |
ACTR5|79913 | -6.8 | 3.975e-09 | 7.09e-05 | 0.7757 |
SDR16C5|195814 | 6.94 | 3.987e-09 | 7.11e-05 | 0.781 |
PLAGL2|5326 | -7.46 | 4.012e-09 | 7.16e-05 | 0.8484 |
CHMP4B|128866 | -7.22 | 5.549e-09 | 9.9e-05 | 0.8443 |
PATHOLOGY.T | Mean (SD) | 2.83 (0.63) |
N | ||
T1 | 6 | |
T2 | 38 | |
T3 | 128 | |
T4 | 18 | |
Significant markers | N = 0 |
PATHOLOGY.N | Mean (SD) | 0.59 (0.79) |
N | ||
N0 | 114 | |
N1 | 41 | |
N2 | 36 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
CD2BP2|10421 | 0.3592 | 3.347e-07 | 0.00597 |
PATHOLOGICSPREAD(M) | Labels | N |
M0 | 159 | |
M1 | 28 | |
M1A | 2 | |
Significant markers | N = 0 |
TUMOR.STAGE | Mean (SD) | 2.37 (0.95) |
N | ||
Stage 1 | 35 | |
Stage 2 | 73 | |
Stage 3 | 50 | |
Stage 4 | 27 | |
Significant markers | N = 0 |
-
Expresson data file = COAD.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Clinical data file = COAD.clin.merged.picked.txt
-
Number of patients = 192
-
Number of genes = 17848
-
Number of clinical features = 9
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.