This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 9 clinical features across 69 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
-
11 genes correlated to 'GENDER'.
-
DDX3Y , RPS4Y1 , RPS4Y2 , EIF1AY , JARID1D , ...
-
10 genes correlated to 'HISTOLOGICAL.TYPE'.
-
TLE6 , FBXO2 , PLCB2 , AGR3 , RAB27B , ...
-
16 genes correlated to 'COMPLETENESS.OF.RESECTION'.
-
CASQ2 , LDB3 , NNAT , PSD , STMN4 , ...
-
2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
-
ACMSD , LHFPL3
-
No genes correlated to 'Time to Death', 'AGE', 'DISTANT.METASTASIS', 'LYMPH.NODE.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.
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=11 | male | N=11 | female | N=0 |
HISTOLOGICAL TYPE | t test | N=10 | rectal mucinous adenocarcinoma | N=8 | rectal adenocarcinoma | N=2 |
DISTANT METASTASIS | t test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=0 | ||||
COMPLETENESS OF RESECTION | ANOVA test | N=16 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=2 |
Time to Death | Duration (Months) | 0.9-52 (median=4) |
censored | N = 40 | |
death | N = 4 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 66.62 (11) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 31 | |
MALE | 38 | |
Significant markers | N = 11 | |
Higher in MALE | 11 | |
Higher in FEMALE | 0 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
DDX3Y | 12.63 | 2.827e-19 | 5.04e-15 | 0.9635 |
RPS4Y1 | 12 | 2.772e-17 | 4.94e-13 | 0.9228 |
RPS4Y2 | 11.53 | 1.686e-16 | 3e-12 | 0.9635 |
EIF1AY | 11 | 1.948e-16 | 3.47e-12 | 0.9576 |
JARID1D | 10.56 | 7.559e-16 | 1.35e-11 | 0.9482 |
CYORF15A | 10.06 | 1.466e-14 | 2.61e-10 | 0.9465 |
UTY | 8.06 | 3.114e-11 | 5.55e-07 | 0.9134 |
CYORF15B | 7.86 | 5.263e-11 | 9.37e-07 | 0.9049 |
ZFY | 7.56 | 1.75e-10 | 3.12e-06 | 0.893 |
TTTY14 | 5.79 | 2.479e-07 | 0.00441 | 0.9011 |
HISTOLOGICAL.TYPE | Labels | N |
RECTAL ADENOCARCINOMA | 58 | |
RECTAL MUCINOUS ADENOCARCINOMA | 7 | |
Significant markers | N = 10 | |
Higher in RECTAL MUCINOUS ADENOCARCINOMA | 8 | |
Higher in RECTAL ADENOCARCINOMA | 2 |
T(pos if higher in 'RECTAL MUCINOUS ADENOCARCINOMA') | ttestP | Q | AUC | |
---|---|---|---|---|
TLE6 | 13.32 | 1.328e-18 | 2.37e-14 | 0.9828 |
FBXO2 | -7.35 | 8.488e-10 | 1.51e-05 | 0.8522 |
PLCB2 | 7.42 | 4.681e-08 | 0.000834 | 0.9163 |
AGR3 | 6.7 | 2.069e-07 | 0.00369 | 0.8695 |
RAB27B | 6.58 | 2.286e-07 | 0.00407 | 0.8695 |
BACE2 | 6.35 | 2.907e-07 | 0.00518 | 0.8473 |
OXCT1 | 5.87 | 7.735e-07 | 0.0138 | 0.9015 |
CARD6 | 6.01 | 9.658e-07 | 0.0172 | 0.8399 |
USP42 | -5.76 | 1.952e-06 | 0.0348 | 0.8399 |
TTLL7 | 7.32 | 1.956e-06 | 0.0348 | 0.9458 |
DISTANT.METASTASIS | Labels | N |
M0 | 57 | |
M1 | 12 | |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 42 | |
N1 | 14 | |
N1A | 1 | |
N2 | 12 | |
Significant markers | N = 0 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 57 | |
R1 | 1 | |
R2 | 10 | |
Significant markers | N = 16 |
ANOVA_P | Q | |
---|---|---|
CASQ2 | 8.109e-11 | 1.44e-06 |
LDB3 | 3.545e-10 | 6.31e-06 |
NNAT | 7.166e-10 | 1.28e-05 |
PSD | 1.319e-08 | 0.000235 |
STMN4 | 2.034e-08 | 0.000362 |
DMN | 7.983e-08 | 0.00142 |
GPM6A | 5.838e-07 | 0.0104 |
MYH3 | 6.403e-07 | 0.0114 |
SYT4 | 7.534e-07 | 0.0134 |
KIAA1881 | 1.054e-06 | 0.0188 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.19 (5.1) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 18 | |
STAGE II | 3 | |
STAGE IIA | 20 | |
STAGE III | 2 | |
STAGE IIIB | 10 | |
STAGE IIIC | 4 | |
STAGE IV | 11 | |
Significant markers | N = 2 |
-
Expresson data file = READ-TP.medianexp.txt
-
Clinical data file = READ-TP.clin.merged.picked.txt
-
Number of patients = 69
-
Number of genes = 17814
-
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.