Table 5 Progression model with top probes associated with gene expression changes

From: Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease

Variablea

Base modelb

Base modelb + kidney promoter probe cg24818418 – Gene EGF (D)

Base modelb + kidney inactive probe cg21048700 -- Gene COL3A1 (E)

% Explained by variablec in base model

% Explained by variablec in model D

% Explained by variablec in model E

Baseline GFR

0.03***

0.04***

0.03***

20.67

30.78

22.03

Diabetes

−0.72*

−1.09***

−1.17 ***

5.75

8.87

10.75

Age

−0.03

−0.01

−0.01

6.16

0.16

1.11

CpG probe

NA

1.24***

−1.21***

NA

17.99

13.02

Methylation batch

NA

NA

 

NA

10.71

11.26

Bisulfite conversion

NA

20.28*

17.70

NA

2.90

2.46

R 2

0.51

0.75

0.70

   

Adjusted R2

0.49

0.70

0.63

   

Akaike information criterion

206.1

177.1

191.1

   

P-value

3.13e−10

5.58e−13

1.126e−10

   
  1. a For each variable, coefficient estimates are shown with the following significance codes: 0 ‘***’; 0.001 ‘**’; 0.01 ‘*’; 0.05 ‘·’
  2. b Model is a weighted linear regression model of adjusted eGFR slope (weight = inverse variance of adjusted eGFR slope). Base model includes variables: baseline eGFR, Diabetes, and Age. Models D and E include base variables with the addition of methylation level at probe location, methylation batch, and bisulfite conversion efficiency
  3. c Proportion of variance explained by the variable based on conditional sum of squares calculated in Type II ANOVA analysis
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