Figure 2: Combinational analysis of transcriptome/DNA microarray and microRNA array datasets to predict possible effects of shikonin on mouse skin tissue. (a) Functional analysis and prediction by “GeneGo Pathway Maps” processed by MetaCore software. By analyzing the [ value] value of different gene-clustering groups in the 24 h treatment datasets obtained from the transcriptomic array and microRNA array analyses, the regulation of the EMT process was predicted to be the major physiological response to shikonin stimulation. The orange and blue bars indicate the calculated value output from transcriptomic array and microRNA array analysis, respectively. (b) Putative signaling networks (microRNA-dependent inhibition of EMT) involved in the modulatory effect of shikonin on skin tissue were predicted from the MetaCore software. In this map, a prototypical cell was constructed from six representative microRNAs and three differentially expressed genes that respond coordinately to an in vivo treatment with shikonin for 24 h. Experimental data from transcriptomic array and microRNA array analyses are linked to and visualized on the maps as thermometer-like symbols. Red and blue scales indicate the upregulated and downregulated gene expressions (microRNAs or mRNAs). M: microRNA binding. TR: transcription regulation. TCF8 (Zeb1): transcription factor 8. SIP1 (Zeb2; Zfhx1B): Smad-interacting protein 1.