Table 1

Comparison of iMM904 and iLL672 gene deletion predictions and experimental data under minimal media conditions.

Media

Model

Method

True viable

False viable

False lethal

True lethal

True viable %

False viable %

MCC


Glucose

iMM904 full

FBA

647

10

32

33

95.29

23.26

0.60

iMM904 full

linMOMA

644

10

35

33

94.85

23.26

0.58

iMM904 full

MOMA

644

10

35

33

94.85

23.26

0.58

iMM904 reduced

FBA

440

9

28

33

94.02

21.43

0.61

iMM904 reduced

linMOMA

437

9

31

33

93.38

21.43

0.60

iMM904 reduced

MOMA

437

9

31

33

93.38

21.43

0.60

iLL672 full

MOMA

433

9

35

33

92.52

21.43

0.57


Galactose

iMM904 full

FBA

595

32

36

59

94.29

35.16

0.58

iMM904 full

linMOMA

595

32

36

59

94.29

35.16

0.58

iMM904 full

MOMA

595

32

36

59

94.29

35.16

0.58

iMM904 reduced

FBA

409

12

33

56

92.53

17.65

0.67

iMM904 reduced

linMOMA

409

12

33

56

92.53

17.65

0.67

iMM904 reduced

MOMA

409

12

33

56

92.53

17.65

0.67

iLL672 full

MOMA

411

19

31

49

92.99

27.94

0.61


Glycerol

iMM904 full

FBA

596

43

36

47

94.30

47.78

0.48

iMM904 full

linMOMA

595

44

37

46

94.15

48.89

0.47

iMM904 full

MOMA

598

44

34

46

94.62

48.89

0.48

iMM904 reduced

FBA

410

20

34

46

92.34

30.30

0.57

iMM904 reduced

linMOMA

409

21

35

45

92.12

31.82

0.56

iMM904 reduced

MOMA

412

21

32

45

92.79

31.82

0.57

iLL672 full

MOMA

406

20

38

46

91.44

30.30

0.55


Ethanol

iMM904 full

FBA

593

45

29

55

95.34

45.00

0.54

iMM904 full

linMOMA

592

45

30

55

95.18

45.00

0.54

iMM904 full

MOMA

592

44

30

56

95.18

44.00

0.55

iMM904 reduced

FBA

408

21

27

54

93.79

28.00

0.64

iMM904 reduced

linMOMA

407

21

28

54

93.56

28.00

0.63

iMM904 reduced

MOMA

407

20

28

55

93.56

26.67

0.64

iLL672 full

MOMA

401

13

34

62

92.18

17.33

0.68


MCC, Matthews correlation coefficient (see Methods). Note that the iLL672 predictions were obtained directly from [3] and thus the viability threshold was not optimized using the maximum MCC approach.

Mo et al. BMC Systems Biology 2009 3:37   doi:10.1186/1752-0509-3-37

Open Data