Table 3. Correlations of different Methods for function prediction for non-synonymous mutations causing diabetes [Spearman's ρ (P value)].

Methods	phyloP	GERP++ RS	SiPhy	SIFT	PolyPhen-2 HDIV	PolyPhen-2 HVAR	LRT	MutationTaster	Mutation Assessor	FATHMM	RadialSVM score
GERP++ RS	0.798 (P = 1.13E-218)
SiPhy	0.857 (P = 2.42E-285)	0.718 (P = 1.15E-156)
SIFT	0.018 (P = 5.92E-01)	0.062 (P = 6.75E-02)	0.087 (P = 1.09E-02)
PolyPhen-2 HDIV	0.228 (P = 1.16E-11)	0.192 (P = 1.20E-08)	0.278 (P = 9.60E-17)	0.506 (P = 8.57E-57)
PolyPhen-2 HVAR	0.205 (P = 1.27E-09)	0.19 (P = 1.85E-08)	0.233 (P = 3.89E-12)	0.496 (P = 2.10E-54)	0.88 (P = 3.88E-281)
LRT	0.332 (P = 3.28E-23)	0.412 (P = 5.32E-36)	0.388 (P = 9.10E-32)	0.252 (P = 1.23E-13)	0.38 (P = 2.13E-30)	0.398 (P = 1.58E-33)
MutationTaster	0.298 (P = 7.40E-21)	0.33 (P = 1.82E-25)	0.339 (P = 6.75E-27)	0.288 (P = 7.50E-18)	0.348 (P = 6.44E-26)	0.354 (P = 6.86E-27)	0.332 (P = 2.93E-23)
Mutation Assessor	0.089 (P = 8.79E-03)	0.158 (P = 3.00E-06)	0.158 (P = 3.03E-06)	0.633 (P = 3.11E-96)	0.516 (P = 3.30E-59)	0.493 (P = 2.16E-53)	0.409 (P = 2.73E-35)	0.321 (P = 2.58E-22)
FATHMM	0.071 (P = 3.75E-02)	0.042 (P = 2.13E-01)	0.087 (P = 1.07E-02)	0.27 (P = 1.09E-15)	0.297 (P = 5.62E-19)	0.342 (P = 5.75E-25)	0.126 (P = 2.28E-04)	0.13 (P = 1.32E-04)	0.297 (P = 8.20E-19)
RadialSVM score	0.188 (P = 2.08E-08)	0.233 (P = 2.51E-12)	0.254 (P = 1.84E-14)	0.492 (P = 2.33E-53)	0.516 (P = 6.04E-60)	0.473 (P = 2.46E-49)	0.268 (P = 2.29E-15)	0.275 (P = 8.71E-17)	0.398 (P = 1.97E-34)	0.409 (P = 4.23E-36)
LR score	0.21 (P = 3.08E-10)	0.211 (P = 2.74E-10)	0.272 (P = 1.96E-16)	0.548 (P = 1.82E-68)	0.603 (P = 9.85E-87)	0.621 (P = 5.02E-93)	0.344 (P = 5.86E-25)	0.303 (P = 3.77E-20)	0.646 (P = 6.66E-104)	0.852 (P = 5.43E-244)	0.634 (P = 3.56E-100)