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Table 2 Pearson’s correlation analysis of RIDGE properties versus normalized mean distances

From: Gene repositioning within the cell nucleus is not random and is determined by its genomic neighborhood

 

Lower CI

Upper CI

R

p value

(A) Differentiation system

 Locus–periphery

Myoblast (MB)

RIDGE

Number of CpG islands

−1

0.900

0.692

0.987

% GC content

0.204

1

0.680

0.015

Genes within region

−1

0.884

0.648

0.979

% SINE

0.307

1

0.735

0.008

% LINE

−1

0.030

−0.531

0.057

Myotube (MT)

RIDGE

Number of CpG islands

−0.248

1

0.352

0.159

% GC content

−0.425

1

0.167

0.322

Genes within region

−0.206

1

0.391

0.132

% SINE

−0.060

1

0.509

0.066

% LINE

−1

1

−0.271

0.224

 Locus–chromocenter

Myoblast (MB)

RIDGE

Number of CpG islands

−0.502

1

0.070

0.424

% GC content

−0.501

1

0.071

0.423

Genes within region

−0.645

1

−0.145

0.655

% SINE

−0.290

1

0.312

0.190

% LINE

−1

0.329

−0.273

0.223

Myotube (MT)

RIDGE

Number of CpG islands

−0.059

1

0.510

0.066

% GC content

0.071

1

0.600

0.033

Genes within region

−0.105

1

0.475

0.083

% SINE

0.128

1

0.635

0.024

% LINE

−1

0.054

−0.514

0.064

(B) Ectopic system

 Locus–periphery

Low MeCP2 level

RIDGE

Number of CpG islands

−1

0.925

0.709

0.975

% GC content

−1

0.894

0.609

0.946

Genes within region

−1

0.913

0.668

0.965

% SINE

−1

0.916

0.680

0.965

% LINE

−0.899

1

−0.624

0.951

High MeCP2 level

RIDGE

Number of CpG islands

−1

0.917

0.683

0.969

% GC content

−1

0.911

0.663

0.964

Genes within region

−1

0.883

0.575

0.932

% SINE

−1

0.891

0.597

0.941

% LINE

−0.899

1

−0.626

0.952

 Locus–chromocenter

Low MeCP2 level

RIDGE

Number of CpG islands

−0.634

1

−0.012

0.512

% GC content

−0.662

1

−0.060

0.556

Genes within region

−0.670

1

−0.075

0.570

% SINE

−0.628

1

−0.002

0.502

% LINE

−1

0.672

0.079

0.573

High MeCP2 level

RIDGE

Number of CpG islands

−0.717

1

−0.165

0.652

% GC content

−0.788

1

−0.318

0.779

Genes within region

−0.673

1

−0.081

0.576

% SINE

−0.658

1

−0.053

0.550

% LINE

−1

0.755

0.244

0.720

  1. Overview of Pearson’s correlation analysis in the differentiation (A) and ectopic MeCP2 system (B) (Fig. 3). For a 2-Mbp window around the gene of interest, the normalized mean distances toward the indicated heterochromatin compartment were correlated to RIDGE and anti-RIDGE properties. RIDGE properties include: number of CpG island, % of GC content, number of genes within the region and % of SINEs; % of LINES (italics) are defined as anti-RIDGES. For each correlation p values, upper and lower confidences were calculated
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Epigenetics & Chromatin

ISSN: 1756-8935