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. 2020 Oct 19;11:5270. doi: 10.1038/s41467-020-18965-w

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© The Author(s) 2020

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. 3 — a MA-Plot showing all genes with differential 5hmC representation. Red and green, respectively denote increased or decreased 5hmC density in PDAC compared to non-cancer with adjusted p-value <0.01, derived by Benjamini–Hochberg method. b IGV genome browser snapshot of YAP1 locus showing the increased 5hmC signal intensity in PDAC samples compared to non-cancer controls. c GSEA of 794 genes with the most statistically significant differential 5hmC representation (adjusted p-value < 0.01, by Benjamini–Hochberg method) and filtered for fold change in 5hmC representation (|(5hmC-PDAC/5hmC-non-cancer)| ≥ 1.5) and minimum average expression (log2(average representation) ≥ 3.5) in PDAC cfDNA as compared to non-cancer samples. Log10 FDR values are derived from Kolmogorov–Smirnov test. Pathways with represented in genes with increased and decreased 5hmC are denoted with red and green, respectively. d MDS of pancreatic cancer (orange) and non-cancer (blue) cfDNA samples using 11,855 genes with statistically significant (adjusted p-value < 0.01, Benjamini–Hochberg method) increase or decrease in 5hmC. Note reasonable partitioning of PDAC from non-cancer samples. e, f MDS of pancreatic cancer (orange) and non-cancer (blue) cfDNA samples from this study (e) and Song et al. (f) using 794 genes with statistically significant differential 5hmC representation (adjusted p-value < 0.01, Benjamini–Hochberg method) and filtered for fold change in 5hmC representation (|(5hmC-PDAC/5hmC-non-cancer)| ≥ 1.5) and minimum average expression (log2(average representation) ≥ 3.5).