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Table 4 CGI profiles: Attribute values of each non-redundant CGI profile.

From: Profile analysis and prediction of tissue-specific CpG island methylation classes

  Constitutively methylated Unmethylated in sperm Differentially methylated Constitutively unmethylated
Attributes 1 2 3 4 5 6 7 8 9
CpGcluster p-value1 0.112 0.130 0.229 0.047 0.020 0.024 0.042 0.033 0.053
O/E ratio1 0.239 0.253 0.380 0.263 0.255 0.241 0.239 0.208 0.269
CpG distance1 0.468 0.439 0.345 0.510 0.419 0.382 0.353 0.374 0.286
SD1 0.506 0.518 0.501 0.578 0.578 0.616 0.594 0.556 0.625
G+C content1 0.336 0.347 0.438 0.259 0.335 0.405 0.474 0.481 0.567
Repetitive content2 0.010 0.000 0.002 0.006 0.005 0.017 0.036 0.042 0.119
Repetitive elements2 0.004 0.000 0.004 0.012 0.004 0.037 0.066 0.078 0.192
PhastCon content3 0.722 0.700 0.521 0.063 0.057 0.102 0.101 0.081 0.092
PhastCon elements3 0.330 0.336 0.242 0.049 0.060 0.076 0.064 0.066 0.050
CG4 0.097 0.101 0.222 0.082 0.104 0.120 0.138 0.130 0.179
GC4 0.203 0.215 0.267 0.149 0.195 0.245 0.255 0.230 0.318
AA4 0.171 0.156 0.141 0.342 0.211 0.172 0.130 0.118 0.088
TT4 0.181 0.239 0.154 0.327 0.352 0.212 0.160 0.158 0.162
TA4 0.325 0.350 0.212 0.323 0.225 0.194 0.160 0.180 0.116
AT4 0.247 0.305 0.211 0.404 0.303 0.221 0.149 0.119 0.161
CA4 0.485 0.391 0.363 0.407 0.320 0.360 0.340 0.358 0.208
TG4 0.540 0.525 0.383 0.386 0.446 0.453 0.415 0.375 0.460
AC4 0.465 0.351 0.399 0.477 0.361 0.379 0.340 0.305 0.193
GT4 0.446 0.410 0.456 0.391 0.420 0.338 0.329 0.363 0.329
AG4 0.467 0.447 0.360 0.498 0.413 0.465 0.448 0.401 0.360
CT4 0.463 0.493 0.443 0.437 0.532 0.492 0.436 0.445 0.401
CC4 0.303 0.323 0.277 0.303 0.330 0.337 0.384 0.469 0.324
GG4 0.296 0.322 0.292 0.311 0.339 0.366 0.423 0.394 0.602
GA4 0.381 0.359 0.306 0.429 0.336 0.376 0.362 0.298 0.270
TC4 0.352 0.355 0.417 0.350 0.393 0.314 0.299 0.378 0.213
Bending5 0.597 0.596 0.567 0.376 0.507 0.639 0.695 0.699 0.789
Curvature5 0.506 0.547 0.410 0.669 0.712 0.653 0.545 0.561 0.405
Stacking energy5 0.771 0.776 0.671 0.840 0.790 0.739 0.711 0.721 0.666
Turns5 0.923 0.920 0.799 0.938 0.943 0.942 0.925 0.928 0.908
Degree of twist5 0.920 0.916 0.794 0.936 0.940 0.940 0.921 0.925 0.903
DNA cleavage5 0.192 0.187 0.234 0.139 0.160 0.191 0.209 0.189 0.285
Bases per turn5 0.074 0.078 0.195 0.060 0.055 0.057 0.073 0.070 0.090
Twist constraint5 0.763 0.749 0.635 0.837 0.780 0.768 0.736 0.724 0.654
Tilt constraint5 0.645 0.657 0.565 0.714 0.729 0.725 0.738 0.768 0.683
Roll constraint5 0.484 0.504 0.467 0.453 0.522 0.572 0.547 0.471 0.652
Shift constraint5 0.606 0.592 0.527 0.721 0.683 0.672 0.674 0.696 0.587
Slide constraint5 0.611 0.606 0.677 0.678 0.652 0.645 0.578 0.469 0.662
Rise constraint5 0.536 0.571 0.466 0.548 0.617 0.649 0.631 0.583 0.691
  1. The attribute values in Table 4 are normalized between 0 and 1. This normalization is performed before the clustering process in order to prevent biased clusters caused by attributes with high absolute values. The significance at a p < 0.05 is relative to these normalized values. The non-normalized values are available in the supplementary information. The attribute values mentioned during the comparison of the profiles are marked in bold and all differences between profiles are supported by a MWW p-value lower than 0.01.
  2. 1CGI-specific attributes; 2Repetitive sequences; 3Evolutionary conservation; 4Dinucleotide content; 5Structural and physicochemical properties;
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