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Table 2 Computational analysis of genes involved in cancer-specific recurrent translocations reveals characteristics of chromosomal fragile sites

From: Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites

  FlexStab MFOLD
Gene Number of flexibility peaks/Kb % A/T % AT-dinucleotides Lowest ΔG valuea (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 ± 1.4c 21 ± 0.5c  
Control 1/100b 61 ± 3.6c 8 ± 1.0c -41.79d
  1. aLowest ΔG value, predicted by MFOLD
  2. bMishmar et al. [17] examined 1.1 Mb of non-fragile DNA, and showed that regions with significantly high flexibility occur every ~100 kb.
  3. cZlotorynski et al. [18]
  4. dThe LAMA4 sequence was randomized 1000 times to serve as a control, and then analyzed by MFOLD.