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. 2020 Jul 21;11(7):e00210. doi: 10.14309/ctg.0000000000000210

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© 2020 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of The American College of Gastroenterology

This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

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Figure 5. — Healthy controls. (a) Scatterplot of transcriptome-wide LFC between TUM and control samples, where control samples are HLT (x axis) or NAT samples (y axis). Colors indicate genes potentially masked (green), misleadingly highlighted (bluish-green), or unaffected (red) by field effect. (b) GSEA results for the 3,856 genes differentially expressed specifically between TUM and HLT and not between TUM and NAT samples; darker colors demonstrate enrichment at FDR 5% in both HLT specific and TUM vs NAT DGE results. Purple and red show discordant and concordant results, respectively. Only hallmark sets with absolute NES >1.5 are shown. (c) Box plots of batch-adjusted counts for C9orf16, 1 of 23 novel TUM-specific genes discovered in this mega-analysis. (d) Overall survival curves for C9orf16 high- and low-expression groups from previously published TCGA data downloaded from the Human Protein Atlas. FDR, false discovery rate; GSEA, gene set enrichment analysis; HLT, healthy; LFC, log2 fold change; NAT, normal-adjacent-to-tumor; NES, normalized enrichment score; TCGA, The Cancer Genome Atlas; TUM, tumor.