Table 4

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

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


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.

1CGI-specific attributes; 2Repetitive sequences; 3Evolutionary conservation; 4Dinucleotide content; 5Structural and physicochemical properties;

Previti et al. BMC Bioinformatics 2009 10:116   doi:10.1186/1471-2105-10-116

Open Data