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Table 2 Correlations

From: Challenging popular tools for the annotation of genetic variations with a real case, pathogenic mutations of lysosomal alpha-galactosidase

Category

Name

Pearson’s r

p-value

B

SIFT

− 0.493

7.87E-19

B

LRT

−0.486

2.76E-18

B

MutationAssessor

−0.573

5.22E-26

B

FATHMM

−0.054

1.85E-01

B

PROVEAN

−0.546

1.86E-23

Meta

VEST3

−0.699

1.08E-42

Meta

MetaSVM

0.285

1.00E + 00

Meta

MetaLR

−0.482

5.77E-18

Meta

M-CAP

−0.255

8.09E-06

ML

POLYPHEN2 HDIV

−0.672

1.67E-38

ML

POLYPHEN2 HVAR

−0.648

4.53E-35

ML

MutationTaster

−0.499

2.42E-19

ML

CADD

−0.595

1.78E-28

ML

DANN

−0.388

8.51E-12

ML

FATHMM-MKL

−0.434

1.35E-14

ML

GenoCanyon

−0.282

7.95E-07

n

GERP++

−0.405

9.34E-13

Cons

phyloP7way vertebrate

−0.441

4.79E-15

Cons

phyloP20way mammalian

−0.214

1.54E-04

Cons

phastCons7way vertebrate

−0.486

2.55E-18

Cons

phastCons 20 way mammalian

−0.256

7.35E-06

Cons

SiPhy 29way logOdds

−0.389

7.65E-12

  1. Pearson’s r correlation coefficient between rank scores and residual activities, together with the associated p-value for significance scoring, for all the predictors used by wANNOVAR. Bold text is used for the highest correlations. Categories are B for “biologically based prediction method”, ML for “Machine Learning based prediction method”, Meta for “Meta prediction method” and Cons for “Conservation scoring tool”