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Table 1 List of the Top and Bottom 7-ranking methylation markers selected as potential biomarkers

From: Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

 

CpG ID

Gene

∆β methylation (tumor - normal)

Correlation (methylation-expression)

AUC

Overall Survival

Top 7

cg10244666

WT1

0.44; p = 2.57e-40

r:0.17; p = 1.09e-6

0,9430 (CI:0.9279–0.9582); p < 0.0001

ns

cg03441279

BCL9

−0.41; p = 5.8e-25

r:-0.32; p = 1.58e-19

0,8434 (CI:0.8184–0.8684); p < 0.0001

ns

cg25025181

SMYD3

−0.45; p = 6.18e-39

r:-0.31; p = 2.36e-19

0,9324 (CI:0.9163–0.9486); p < 0.0001

ns

cg01268824

ZNF154

0.42; p = 4.68e-34

r:-0.63; p = 1.44e-85

0,9002 (CI:0.8778–0.9226); p < 0.0001

p = 0.0097

cg09578475

ZNF177

0.51; p = 4.87e-40

r:0.20; p = 2.73e-8

0,9378 (CI:0.9219–0.9537); p < 0.0001

ns

cg08065231

0.46; p = 9.51e-39

r:0.23; p = 1.54e-10

0,9320 (CI:0.9153–0.9486); p < 0.0001

ns

cg13703871

0.47; p = 2.91e-40

r:0.17; p = 3.13e-6

0,9410 (CI:0.9257–0.9562); p < 0.0001

ns

cg22674699

HOXD9

0.40; p = 3.15e-28

r:-0.17; p = 1.12e-6

0,8679 (CI:0.8427–0.8931); p < 0.0001

p = 0.0381

cg10119075

ITIH5

0.41; p = 1.51e-39

r:-0.26; p = 1.73e-13

0,9397 (CI:0.9243–0.9552); p < 0.0001

ns

Bottom 7

cg15165122

ANKRD53

0.41; p = 2.09e-34

r: −0.48; p = 2.34e-46

0,9028 (CI:0.8827–0.9229); p < 0.0001

ns

cg12743248

EFCAB1

−0.45; p = 5.39e-45

r: 0.44; p = 8.49e-38

0,9664 (CI:0.9553–0.9775); p < 0.0001

ns

cg12374721

PRAC2

0.46; p = 9.42e-36

r:0.39; p = 1.63e-30

0,9118 (CI:0.8923–0.9313); p < 0.0001

p = 0.0134

cg27170427

RIMBP2

−0.46; p = 1.24e-46

r:0.35; p = 1.79e-24

0,9766 (CI:0.9680–0.9851); p < 0.0001

ns

cg17192862

−0.41; p = 1.29e-46

r:0.45; p = 6.74e-40

0,9765 (CI:0.9675–0.9856); p < 0.0001

ns

cg10224098

RNF220

0.45; p = 1.01e-39

r:-0.09; p = 1.51e-2

0,9393 (CI:0.9220–0.9566); p < 0.0001

ns

cg18081940

TDRD10

0.41; p = 1.58e-39

r:-0.20; p = 4.17e-8

0,9360 (CI:0.9189–0.9531); p < 0.0001

p = 0.0037

cg10216717

TMEM132C

−0.45; p = 2.02e-49

r:0.46; p = 3.44e-42

0,9920 (CI:0.9872–0.9968); p < 0.0001

ns

cg04475027

0.42; p = 1.19e-40

r:-0.23; p = 3.24e-11

0,9446 (CI:0.9289–0.9604); p < 0.0001

p = 0.0291

  1. ns not significant
  2. The “Top 7” and “Bottom 7” genes (based on OncoScore results) selected for analysis as potential methylation biomarkers