Table 5

Prediction of the disease type with a SVM-based method

Encoding

Q

MCC

Sp(C)

Sn(C)

Sp(O)

Sn(O)


mut_E_W1

0.59

0.12

0.21

0.55

0.88

0.60


mut_E_W5

0.64

0.17

0.24

0.55

0.88

0.66


OnlyGO

0.89

0.60

0.7

0.63

0.93

0.95


mut_GO_E

0.89

0.60

0.68

0.65

0.93

0.94


mut_GO_E_W1

0.89

0.58

0.68

0.64

0.93

0.94


mut_GO_E_W5

0.89

0.58

0.68

0.64

0.93

0.94


mut_GO

0.90

0.61

0.69

0.66

0.93

0.94


mut= is a 20 elements vector that encodes for the variation type; Wx= a input sequence window of dimension x centered into the variation; E= the evolutionary information on the variation obtained by extracting the 4 columns that represent the wild-type and the mutant residues as reported by PSI-BLAST PSSM/PROFILE output (-Q option); GO= the 3 GO scores. For a definition of classes and scoring indexes see section: Measuring the performance.

Martelli et al. BMC Genomics 2012 13(Suppl 4):S8   doi:10.1186/1471-2164-13-S4-S8

Open Data