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. 2020 Jun 29;20:298. doi: 10.1186/s12870-020-02511-3

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© The Author(s) 2020

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. 8 — The extracted cold responsive GRN comprising of direct and indirect targets of DE miRNAs. (a) Network of miRNAs and targets that are differentially expressed at any one of the analyzed time points (FC ≥ 2& ≤ − 2, Benjamini-Hochberg corrected p-value ≤0.05). Functional modules associated with cold acclimation, kinase signaling, transcription; translation and transport are represented by blue, dark green, pink, and orange color, respectively. (blue nodes = miRNAs, orange nodes = TFs, gray nodes = targets) (b) Subnetwork of miR858. (c) Subnetwork of miR319. In (b) and (c) direct and indirect targets of miRNAs are differentially expressed in at least one of the analyzed time points (FC ≥ 2& ≤ − 2, Benjamini-Hochberg corrected p-value ≤0.05). Curved edges indicate regulatory connections of a regulator and its target. The node colors depict the inferred function based on GO enrichment analyses. Green: biotic stress, cell organization; blue: cold stress; pink: transcription, translation; orange: transport, PPR; dark blue: cell wall, lignin synthesis; red: signaling, protein degradation. The data related to GRN can be accessed through GEPHI Software (Additional file 7: Data S2)