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. 2020 Oct 15;10:17483. doi: 10.1038/s41598-020-74564-1

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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 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/.

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Transcriptome-wide expression noise as an indicator for differential expressions. (a) Expression noise between 2 replicates at the same time point (between replicate 1 and replicate 2 of condition 1, denoted as r1_c1/r2_c1 and between replicate 1 and replicate 2 of condition 2, denoted as r1_c2/r2_c2) and between anchor and target conditions in 4 combinations of 2 replicates and 2 conditions, after the removal of lowly expressed genes (Fig. S1). (b) Distinction between differentially expressed (DE) genes (green) and non-DE genes (orange) by overlaying expression scatter between 2 conditions and 2 replicates at all conditions in E. coli (left panel), S. cerevisiae (middle panel), and mouse ESC (right panel). (c) Expression noise between anchor and target time points due to DE genes (filled circle) and non-DE genes (filled triangle) with scatter dot size ranging from 0.001 to 0.01 log10(TPM)) in E. coli (left panel), S. cerevisiae (middle panel), and mouse ESC (right panel). Scatter dot size at 0.004 log10(TPM) for E. coli, 0.001 log10(TPM) for S. cerevisiae, and 0.002 log10(TPM) for mouse ESC resulted in non-DE gene set whose expression noise between anchor and target time points is comparable to the averaged whole-transcriptome noise between 2 replicates (dashed blue line). The most conservative dot size of E. coli, 0.004 log10(TPM) was applied for all cell types. (d) Expression noise at scatter dot size 0.004 for transcriptome-wide replicates (Rep), non-DE and DE genes between 2 different conditions.