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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