Co-expression Network:We constructed a co-expression network for L. japonica by calculating the correlation in expression between genes using the Pearson correlation coefficient (PCC). A positive co-expression network with 22233 nodes and 701669 edges and a negative co-expression network with 4235 nodes and 312728 edges were constructed.

Protein Protein Interaction (PPI) Network:We predicted orthologous protein relationships between A. thaliana and L.japonica using InParanoid (Sonnhammer and Ostlund, 2015)(bootstrap >0.6) and mapped the PPI of A. thaliana to L.japonica. We obtained a PPI network of L.japonica with 4415 nodes and 12828 edges.

Gene functional modules:We identified 324 functional modules with 18075 genes by CFinder softward (Adamcsek et al., 2006) and we established that these modules could be annotated with different GO terms, gene families, and KEGG pathways using the GSEA tool (Yi et al., 2013).

Network display with expression view:We introduced this method for displaying differentially expressed genes. For replicated transcriptome samples, we used the fold change of gene expression (|log2foldchange|>1) and Student t-test (p-value <0.05) to calculate differentially expressed genes. In our comparative transcriptome analysis, the up-regulated genes are shown in red and the down-regulated genes are shown in blue. For unreplicated tissue samples, we screened the expressed and non-expressed genes (TPM>0) in each sample to display the network. Expressed and non-expressed genes are marked in green and gray in the network, respectively.

Sonnhammer, E.L., and Ostlund, G. (2015). InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res 43: D234-239.
Adamcsek, B., Palla, G., Farkas, I.J., Derenyi, I., and Vicsek, T. (2006). CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
Yi, X., Du, Z., and Su, Z. (2013). PlantGSEA: a gene set enrichment analysis toolkit for plant community. Nucleic Acids Res 41: W98-103.