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Fig. 4 | Genome Medicine

Fig. 4

From: Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome

Fig. 4

Epigenetic deregulation of lamina-associated domains (LADs) contributes to aberrant gene expression in HGPS. a 50 most differentially (q < 0.05, Benjamini-Hochberg) expressed genes in six HGPS vs. three control samples. Lowly expressed genes are shown in blue, highly expressed ones in red. FPKM = fragments per kilobase of transcript per million mapped reads. b Selection of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and hallmark gene sets enriched (false discovery rate (FDR) q < 0.05) in HGPS fibroblasts. NES = normalized enrichment score. c TRANSFAC transcription factor (TF) network analysis of upstream factors controlling the observed expression changes. d Venn diagram showing numbers of genes overlapping between HGPS young (< 8 years) vs. control samples and HGPS old (> 8 years) vs. control samples, respectively. The GO processes characteristic of each comparison are given. e Median distance to the nearest LAD (lamin A and/or lamin B) for the indicated sets of genes. Numbers of genes in each group and Wilcoxon rank-sum test P values (with continuity correction) are given. *P = 2.25e−4. DNAm = DNA methylation

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