*4.8. CeRNAs Network Analysis of ncRNAs*

A hypergeometric test was executed for each ceRNA pair separately, which was defined by four parameters: (i) N was the total number of miRNAs used to predict targets; (ii) K was the number of miRNAs that interact with the chosen gene of interest; (iii) n was the number of miRNAs that interact with the candidate ceRNA of the chosen gene; (iv) c was the common miRNA number between these two genes. The test calculates the P-value by using the following formula:

$$P = \sum\_{i=c}^{\min(K,n)} \frac{\binom{K}{i} \binom{N-K}{n-i}}{\binom{N}{n}}$$

All *p*-values were subject to false discovery rate (FDR) correction. The following features were necessary for ceRNAs: (i) number of miRNAs that interact with the candidate ceRNA ≥ 5; (ii) FDR < 0.05 [56].

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/7/ 2001/s1.

**Author Contributions:** J.Z. conceived and designed the experiments and wrote the manuscript; Y.W., B.Z., Y.L., Q.W., and L.G. participated in the related experiments and analyzed the data.

**Funding:** This work was supported by the National Natural Science Foundation of China (31772022), the Natural Science Foundation of Beijing (6182016), the National Key Research and Development Program of China (2016YFD0400901), the China Agriculture Research System Project (CARS-23), Special innovation ability construction fund of Beijing Academy of Agricultural and Forestry Sciences (20180404), the Young Investigator Fund of Beijing Academy of Agricultural and Forestry Sciences (201709), Beijing Academy of Agriculture and Forestry fruit and vegetable preservation and processing innovation team (201602), the International Cooperation Fund Project of Beijing Academy of Agricultural and Forestry Sciences.

**Acknowledgments:** The authors acknowledge James Giovannoni (USDA/Cornell) and Lance Courtney (Cornell) for useful discussions during the preparation of this manuscript.

**Conflicts of Interest:** The authors declare no conflict of interest.
