Table 2

Computational analysis of genes involved in cancer-specific recurrent translocations reveals characteristics of chromosomal fragile sites

FlexStab

MFOLD

Gene

Number of flexibility peaks/Kb

% A/T

% AT-dinucleotides

Lowest ΔG value^a (kcal/mol)

CBFB

4/322

79 ± 3.9

24 ± 3.0

-116.91

MYH11

4/404

78 ± 5.5

23 ± 5.9

-97.02

HMGA1

6/259

81 ± 7.8

24 ± 3.6

-124.07

LAMA4

9/397

78 ± 2.7

23 ± 3.0

-59.2

MLL

5/339

78 ± 10.2

23 ± 4.8

-100.74

AFF4

4/338

81 ± 3.3

26 ± 3.1

-100.97

Fragile site

78 ± 1.4^c

21 ± 0.5^c

Control

1/100^b

61 ± 3.6^c

8 ± 1.0^c

-41.79^d

^aLowest ΔG value, predicted by MFOLD

^bMishmar et al. [17] examined 1.1 Mb of non-fragile DNA, and showed that regions with significantly high flexibility occur every ~100 kb.

^cZlotorynski et al. [18]

^dThe LAMA4 sequence was randomized 1000 times to serve as a control, and then analyzed by MFOLD.

Burrow et al. BMC Genomics 2009 10:59   doi:10.1186/1471-2164-10-59