MicroRNAs can affect GRNs directly and indirectly. The regulatory effects of a miRNA are not limited to the direct RISC-dependent targeting. Both direct and indirect targets are integral components of GRNs and should be included in functional analysis. When a miRNA is over-expressed, its direct targets should be down-regulated. If the direct target is a repressor of downstream genes, then as a result of miRNA regulation, these genes will be de-repressed and their levels will go up (Upregulated differentially expressed genes or DEGs). On the other hand, genes downstream of activators and transcription factors will go down accordingly with the direct targets. In addition, proteins that physically associate with direct targets to function together in a complex may also be affected.