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. 2022 Mar 28;23:86. doi: 10.1186/s13059-022-02647-5

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© The Author(s) 2022

Open AccessThis 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. 2 — SCC-related gene modules and co-expression networks in seeds. a Gene correlation network of SCC-related module (M65) at 20 DAF. Phenylpropanoid biosynthesis-related genes significantly associated to SCC detected by TWAS at 20 DAF are labeled in the module. b Gene correlation network of SCC-related modules (M97, M79, M139) at 40 DAF. Phenylpropanoid biosynthesis-related genes significantly associated to SCC detected by TWAS at 40 DAF are labeled in the module. c Correlation between the expression pattern (X-axis) of M65 and SCC (Y-axis). d Correlation between the expression pattern (X-axis) of M139 and SCC (Y-axis). e Correlation network built on the overlapped genes of the TWAS-significant genes, M65 and M139. The green dots represent phenylpropanoid biosynthesis-related transcription factors and red dots represent other phenylpropanoid biosynthesis-related genes, the blue dots represent the rest of genes. The size of a node is proportional to its degree (the number of correlated genes). Genes in a, b, and e are shown by dots and gene-gene correlations (FDR < 0.01) are indicated by gray lines