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Background   In our previous studies, we discovered a series of chalcone-based phytopathogenic fungus inhibitors. However, knowledge of their effects, detailed targets and molecular mechanisms in  Magnaporthe oryzae  ( M. oryzae ) remained limited.    Methods  To explore the expression and function of differentially expressed genes in  M. oryzae  after treatment with compound C1, we analyzed the expression profile of mRNAs using a microarray analysis and GO, KEGG and WGCNA analysis, followed by qRT-PCR and Western blots to validate our findings.    Results  A total of 1013 up-regulated and 995 down-regulated mRNAs were differentially expressed after  M. oryzae  was treated with C1 compared to those of the control samples. Among these, cytochrome P450, glycylpeptide N-myristoyltransferase (NMT) and peroxisomal membrane protein 4 were identified as the most significant DEGs and were validated by experiments.    Conclusion  In conclusion, our study suggests that the combination of transcriptomic microarray, bioinformatics analysis and weighted gene co-expression networks can be used to predict potential therapeutic targets and to map the pathways regulated by small molecular natural product-like drugs.    Electronic supplementary material  The online version of this article (doi:10.1186/s40064-016-3385-9) contains supplementary material, which is available to authorized users.

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Discovery of the molecular mechanisms of the novel chalcone-based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co-expression network analysis