This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 20596 genes and 8 clinical features across 23 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.
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3 genes correlated to 'GENDER'.
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ALG11__1 , UTP14C , KIF4B
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5 genes correlated to 'HISTOLOGICAL.TYPE'.
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ME1 , FGFR1OP , ZNF552 , RBP7 , SPAG8
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14 genes correlated to 'DISTANT.METASTASIS'.
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RAB21 , SETD6 , FAM38A , TTC12 , NTN3 , ...
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15 genes correlated to 'LYMPH.NODE.METASTASIS'.
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C1ORF88 , CCND2 , HNRNPA3 , ANKRD13D , DYRK1B , ...
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79 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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C14ORF73 , HAAO , BEGAIN , GRID1 , ARMC4 , ...
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37 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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ATP6V0E2 , LOC401431 , LOC652276 , HES4 , C4ORF48 , ...
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No genes correlated to 'AGE', 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 | ||
---|---|---|---|---|---|---|
AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=3 | male | N=2 | female | N=1 |
HISTOLOGICAL TYPE | ANOVA test | N=5 | ||||
DISTANT METASTASIS | ANOVA test | N=14 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=15 | ||||
COMPLETENESS OF RESECTION | ANOVA test | N=79 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=37 |
AGE | Mean (SD) | 67.13 (8.6) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 11 | |
MALE | 12 | |
Significant markers | N = 3 | |
Higher in MALE | 2 | |
Higher in FEMALE | 1 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
ALG11__1 | 6.83 | 1.2e-06 | 0.0247 | 0.9697 |
UTP14C | 6.83 | 1.2e-06 | 0.0247 | 0.9697 |
KIF4B | -6.84 | 1.822e-06 | 0.0375 | 0.9924 |
HISTOLOGICAL.TYPE | Labels | N |
PANCREAS-ADENOCARCINOMA DUCTAL TYPE | 20 | |
PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE | 2 | |
PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA | 1 | |
Significant markers | N = 5 |
ANOVA_P | Q | |
---|---|---|
ME1 | 8.002e-19 | 1.65e-14 |
FGFR1OP | 1.005e-14 | 2.07e-10 |
ZNF552 | 3.778e-12 | 7.78e-08 |
RBP7 | 4.832e-12 | 9.95e-08 |
SPAG8 | 1.601e-09 | 3.3e-05 |
DISTANT.METASTASIS | Labels | N |
M0 | 2 | |
M1 | 1 | |
MX | 20 | |
Significant markers | N = 14 |
ANOVA_P | Q | |
---|---|---|
RAB21 | 1.035e-16 | 2.13e-12 |
SETD6 | 4.233e-14 | 8.72e-10 |
FAM38A | 5.286e-13 | 1.09e-08 |
TTC12 | 7.391e-12 | 1.52e-07 |
NTN3 | 1.471e-09 | 3.03e-05 |
TRIM4 | 1.616e-08 | 0.000333 |
SLCO4C1 | 6.074e-08 | 0.00125 |
GUSB | 6.242e-08 | 0.00129 |
KATNAL2__1 | 8.655e-08 | 0.00178 |
TCEB3B | 8.655e-08 | 0.00178 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 8 | |
N1 | 14 | |
N1B | 1 | |
Significant markers | N = 15 |
ANOVA_P | Q | |
---|---|---|
C1ORF88 | 2.575e-13 | 5.3e-09 |
CCND2 | 7.452e-12 | 1.53e-07 |
HNRNPA3 | 1.111e-10 | 2.29e-06 |
ANKRD13D | 3.241e-09 | 6.67e-05 |
DYRK1B | 5.755e-09 | 0.000119 |
SORT1 | 1.501e-08 | 0.000309 |
LHFPL5 | 7.133e-08 | 0.00147 |
ZNF655 | 2.358e-07 | 0.00486 |
BASP1__1 | 2.736e-07 | 0.00563 |
IFNAR1 | 4.618e-07 | 0.00951 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 13 | |
R1 | 9 | |
RX | 1 | |
Significant markers | N = 79 |
ANOVA_P | Q | |
---|---|---|
C14ORF73 | 7.086e-30 | 1.46e-25 |
HAAO | 5.254e-23 | 1.08e-18 |
BEGAIN | 7.541e-19 | 1.55e-14 |
GRID1 | 1.117e-18 | 2.3e-14 |
ARMC4 | 1.231e-17 | 2.53e-13 |
LASS3 | 2.305e-17 | 4.75e-13 |
ZNF230 | 1.349e-16 | 2.78e-12 |
GPATCH2__1 | 1.632e-16 | 3.36e-12 |
SPATA17__1 | 1.632e-16 | 3.36e-12 |
C5ORF42 | 9.036e-16 | 1.86e-11 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.22 (2.7) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE IA | 2 | |
STAGE IB | 1 | |
STAGE IIA | 3 | |
STAGE IIB | 15 | |
STAGE III | 1 | |
STAGE IV | 1 | |
Significant markers | N = 37 |
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Expresson data file = PAAD-TP.meth.by_min_expr_corr.data.txt
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Clinical data file = PAAD-TP.clin.merged.picked.txt
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Number of patients = 23
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Number of genes = 20596
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Number of clinical features = 8
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.