This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 19985 genes and 10 clinical features across 665 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.
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440 genes correlated to 'AGE'.
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KIAA1143 , KIF15 , C1ORF103 , LGALS8 , MEX3C , ...
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41 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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WDR74 , RHBDL3 , FASTKD3 , MTRR__1 , SIL1 , ...
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2 genes correlated to 'PATHOLOGY.N.STAGE'.
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TCP11L1 , ADA
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68 genes correlated to 'PATHOLOGY.M.STAGE'.
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ABCE1 , ANAPC10 , RHBDL3 , FASTKD3 , MTRR__1 , ...
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191 genes correlated to 'GENDER'.
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ALDOC , CRIP1 , NMNAT3 , DNAJC15 , EML1 , ...
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1201 genes correlated to 'HISTOLOGICAL.TYPE'.
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CLUAP1 , RNF25 , STK36 , PRKAR2A , FAR1 , ...
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116 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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PRIM1 , METAP2 , MAEA , HMG20B , ZNF639 , ...
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1 gene correlated to 'NUMBER.OF.LYMPH.NODES'.
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TCP11L1
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No genes correlated to 'Time to Death', and 'PATHOLOGY.T.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=440 | older | N=343 | younger | N=97 |
NEOPLASM DISEASESTAGE | ANOVA test | N=41 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | Spearman correlation test | N=2 | higher stage | N=2 | lower stage | N=0 |
PATHOLOGY M STAGE | ANOVA test | N=68 | ||||
GENDER | t test | N=191 | male | N=54 | female | N=137 |
HISTOLOGICAL TYPE | ANOVA test | N=1201 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=116 | yes | N=47 | no | N=69 |
NUMBER OF LYMPH NODES | Spearman correlation test | N=1 | higher number.of.lymph.nodes | N=1 | lower number.of.lymph.nodes | N=0 |
Time to Death | Duration (Months) | 0-234.3 (median=21.4) |
censored | N = 585 | |
death | N = 74 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 58.06 (13) |
Significant markers | N = 440 | |
pos. correlated | 343 | |
neg. correlated | 97 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
KIAA1143 | 0.3293 | 5.277e-18 | 1.05e-13 |
KIF15 | 0.3293 | 5.277e-18 | 1.05e-13 |
C1ORF103 | 0.3106 | 4.285e-16 | 8.56e-12 |
LGALS8 | -0.3097 | 5.259e-16 | 1.05e-11 |
MEX3C | 0.2998 | 4.805e-15 | 9.6e-11 |
C20ORF199 | 0.2972 | 8.42e-15 | 1.68e-10 |
SNORD12 | 0.2972 | 8.42e-15 | 1.68e-10 |
C9ORF69 | 0.2856 | 9.625e-14 | 1.92e-09 |
DNMT3A | 0.2854 | 1.001e-13 | 2e-09 |
CACNA2D1 | 0.2839 | 1.362e-13 | 2.72e-09 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 49 | |
STAGE IA | 55 | |
STAGE IB | 5 | |
STAGE II | 8 | |
STAGE IIA | 212 | |
STAGE IIB | 155 | |
STAGE III | 2 | |
STAGE IIIA | 107 | |
STAGE IIIB | 17 | |
STAGE IIIC | 43 | |
STAGE IV | 6 | |
STAGE X | 5 | |
Significant markers | N = 41 |
ANOVA_P | Q | |
---|---|---|
WDR74 | 1.747e-20 | 3.49e-16 |
RHBDL3 | 2.37e-20 | 4.74e-16 |
FASTKD3 | 7.679e-20 | 1.53e-15 |
MTRR__1 | 7.679e-20 | 1.53e-15 |
SIL1 | 7.436e-19 | 1.49e-14 |
MMAB | 1.421e-17 | 2.84e-13 |
MVK | 1.421e-17 | 2.84e-13 |
ATP5J | 8.599e-17 | 1.72e-12 |
GABPA | 8.599e-17 | 1.72e-12 |
TTC32 | 4.644e-14 | 9.28e-10 |
PATHOLOGY.T.STAGE | Mean (SD) | 1.93 (0.71) |
N | ||
1 | 174 | |
2 | 383 | |
3 | 86 | |
4 | 20 | |
Significant markers | N = 0 |
PATHOLOGY.N.STAGE | Mean (SD) | 0.82 (0.91) |
N | ||
0 | 292 | |
1 | 235 | |
2 | 84 | |
3 | 46 | |
Significant markers | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
PATHOLOGY.M.STAGE | Labels | N |
CM0 (I+) | 1 | |
M0 | 552 | |
M1 | 6 | |
MX | 106 | |
Significant markers | N = 68 |
ANOVA_P | Q | |
---|---|---|
ABCE1 | 4.148e-108 | 8.29e-104 |
ANAPC10 | 4.148e-108 | 8.29e-104 |
RHBDL3 | 1.615e-25 | 3.23e-21 |
FASTKD3 | 2.477e-25 | 4.95e-21 |
MTRR__1 | 2.477e-25 | 4.95e-21 |
MMAB | 1.28e-22 | 2.56e-18 |
MVK | 1.28e-22 | 2.56e-18 |
NHEDC1 | 1.348e-12 | 2.69e-08 |
SAG | 2.353e-12 | 4.7e-08 |
TSTD1 | 1.104e-10 | 2.2e-06 |
GENDER | Labels | N |
FEMALE | 658 | |
MALE | 7 | |
Significant markers | N = 191 | |
Higher in MALE | 54 | |
Higher in FEMALE | 137 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
ALDOC | -30.35 | 2.529e-72 | 5.05e-68 | 0.962 |
CRIP1 | -20.11 | 1.688e-70 | 3.37e-66 | 0.8689 |
NMNAT3 | -14.96 | 3.999e-43 | 7.99e-39 | 0.693 |
DNAJC15 | -14.91 | 5.895e-42 | 1.18e-37 | 0.7093 |
EML1 | -13.13 | 6.565e-35 | 1.31e-30 | 0.6235 |
ADCY5 | 14.21 | 1.343e-31 | 2.68e-27 | 0.7312 |
RND2 | -14.18 | 1.848e-31 | 3.69e-27 | 0.7579 |
SLCO4C1 | -12.8 | 8.868e-30 | 1.77e-25 | 0.7178 |
LOC400043 | -13.5 | 5.202e-29 | 1.04e-24 | 0.5597 |
ACADS | -11.73 | 1.097e-28 | 2.19e-24 | 0.612 |
HISTOLOGICAL.TYPE | Labels | N |
INFILTRATING CARCINOMA NOS | 1 | |
INFILTRATING DUCTAL CARCINOMA | 456 | |
INFILTRATING LOBULAR CARCINOMA | 134 | |
MEDULLARY CARCINOMA | 5 | |
MIXED HISTOLOGY (PLEASE SPECIFY) | 24 | |
MUCINOUS CARCINOMA | 12 | |
OTHER SPECIFY | 32 | |
Significant markers | N = 1201 |
ANOVA_P | Q | |
---|---|---|
CLUAP1 | 0 | 0 |
RNF25 | 1.962e-271 | 3.92e-267 |
STK36 | 1.962e-271 | 3.92e-267 |
PRKAR2A | 3.391e-213 | 6.78e-209 |
FAR1 | 5.401e-100 | 1.08e-95 |
RNF26 | 2.007e-85 | 4.01e-81 |
AP1M2 | 3.802e-81 | 7.6e-77 |
CYB5D1__1 | 1.596e-73 | 3.19e-69 |
LSMD1__1 | 1.596e-73 | 3.19e-69 |
MPDU1 | 1.946e-58 | 3.89e-54 |
116 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 215 | |
YES | 450 | |
Significant markers | N = 116 | |
Higher in YES | 47 | |
Higher in NO | 69 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
PRIM1 | 7.8 | 2.499e-14 | 4.99e-10 | 0.6547 |
METAP2 | 7.36 | 6.498e-13 | 1.3e-08 | 0.6625 |
MAEA | -7.18 | 2.192e-12 | 4.38e-08 | 0.6474 |
HMG20B | -7.13 | 3.126e-12 | 6.25e-08 | 0.648 |
ZNF639 | 6.96 | 8.941e-12 | 1.79e-07 | 0.6478 |
UHRF1BP1L | 6.92 | 1.261e-11 | 2.52e-07 | 0.6578 |
C16ORF58 | -6.9 | 1.807e-11 | 3.61e-07 | 0.6577 |
TSTD1 | -6.52 | 1.689e-10 | 3.37e-06 | 0.6318 |
USF1 | -6.52 | 1.689e-10 | 3.37e-06 | 0.6318 |
SRRM5 | -6.48 | 2.099e-10 | 4.19e-06 | 0.6352 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.58 (4.8) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
TCP11L1 | 0.2267 | 1.392e-08 | 0.000278 |
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Expresson data file = BRCA-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = BRCA-TP.merged_data.txt
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Number of patients = 665
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Number of genes = 19985
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Number of clinical features = 10
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 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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.