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. 2024 Jun 20;17:40. doi: 10.1186/s13041-024-01112-7

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Two examples of DGE, DTE, and DTU for two genes. These cartoon examples portray two genes with three transcript isoforms in two conditions. Both genes have significant DTE, but Gene 1 has no significant DTU (A, C, and E), while Gene 2 has significant DTU (B, D, and F). (A and B) Cartoon examples representing the overall gene expression: (A) shows down-regulation of Gene 1 in condition one compared to condition two, and (B) shows about equal expression of Gene 2 across both conditions. (C and D) Cartoon examples representing transcript isoform expression between the two conditions. (E and F) Cartoon examples showing isoform fraction (IF) in these two genes, where (E) shows no change in IF across the two conditions and, therefore, no significant DTU. (F) Cartoon showing significant changes in IF across conditions, revealing significant DTU. IF is calculated by the number of counts for a specific isoform divided by the total number of read counts for that gene (including all isoforms)