*2.4. Construction of the Competing Endogenous RNAs (ceRNAs) Network*

It is reported that both lncRNAs and circRNAs can interact with miRNAs through microRNA response elements (MREs) within the ceRNA network [32,33]. We developed candidate ceRNA relationships through the miRNA target relationship and obtained 2972 pairs of ceRNA relationships. Then, we extracted three comprehensive ceRNA networks from the ceRNA relationship pairs, including 162 mRNAs, 81 lncRNAs, and 4 circRNAs (Figure 5, Table S7). More importantly, several important enzymes and transcription factors involved in chilling injury, such as ATPase, serine/threonine protein kinase, β-galactosidase, heat shock protein, ethylene-responsive transcription factor, were found in the ceRNA network in our results, indicating their specific cooperative regulation roles in chilling stress (Table S7). In addition, the functions of the key genes were annotated, and the first few most significantly enriched pathways were selected to extract the relationships between genes in multiple pathways and to integrate them into a pathway network. In the network, the key genes in the pathway are involved in lipid transport and metabolism which is important in the chilling stress process (Figure 6, Table S8).

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**Figure 5.** The ceRNA networks of mRNAs, lncRNAs, and circRNAs were parsed, and ceRNA relationship pairs were obtained, including 162 mRNAs, 81 lncRNAs, and 4 circRNAs. **Figure 5.** The ceRNA networks of mRNAs, lncRNAs, and circRNAs were parsed, and ceRNA relationship pairs were obtained, including 162 mRNAs, 81 lncRNAs, and 4 circRNAs.

*Int. J. Mol. Sci.* **2018**, *19*, x FOR PEER REVIEW 8 of 15

**Figure 6.** Pathway network from the annotation of the key genes. The key genes in the pathway are involved in lipid transport and metabolism, which play an important role in the chilling stress process. **Figure 6.** Pathway network from the annotation of the key genes. The key genes in the pathway are involved in lipid transport and metabolism, which play an important role in the chilling stress process.
