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. 2019 Jun 6;10:2489. doi: 10.1038/s41467-019-10129-9

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — Gene expression dysregulation domains do not depend on the Down syndrome (DS) genotype. a Plot showing fold change of gene expression on Hsa21 in DS vs euploid human fibroblasts³. Expressed genes (grey dots) are plotted in chromosomal order. A Loess smoothing curve is superimposed with regions that are upregulated or downregulated indicated in red or green, respectively. b Same as a but the fold changes are computed between two DS and two euploid samples vs between two different DS and two different euploid samples. Note apparent regions of upregulation and downregulation in this no-genotype-difference comparison. c, d Plots of flips (c) and energy (d) for comparisons of different combinations of DS and euploid human fibroblast samples arranged such that there is no genotype difference in the comparison. Each dot is a comparison of different combinations of samples with blue indicating combinations that are significantly different (>2 SD) from the mean of bootstrapped chromosomes and black for not significant. Horizontal lines indicate the values obtained for the correct comparison of four DS vs four euploid samples (red, significant; black, not significant)