Development of antifungal drugs is generally considered far more challenging than that of antibacterial drugs since fungi share a number of cellular features with mammalian cells. Therefore, searching for fungal specific virulence factors has been a focus of study in the medical mycology field past decades. Microbial pathogens survive and proliferate in the human host by coordinating their complex pathogenomic signaling network. Here we provide examples for development of novel antifungal therapeutic methods by exploiting transcriptome networks of various signal transduction cascades in human fungal pathogens. In these studies we employed comparative transcriptome and genetics analysis to explore several stress-activated signaling (SAS) pathways, including the HOG (High Osmolarity Glycerol response) pathway and Ras/cAMP-signaling pathway, of Cryptococcus neoformans, which causes life threatening fungal meningitis. Our transcriptome analysis of the HOG pathway revealed that inhibition of the HOG pathway increases expression of ergosterol biosynthesis genes and cellular ergosterol content, conferring a striking synergistic antifungal activity with amphotericin B and providing an excellent opportunity to develop a novel therapeutic method for treatment of cryptococcosis. Another interesting finding of this transcriptome analysis was that HOG-dependent, ubiquitin-proteasome system, are also critical in controlling diverse stress response. Through transcriptome analysis of C. neoformans Ras/cAMP-signaling pathway by DNA microarray, we discovered that a number of environmental stress response genes are differentially modulated in the ras1D and cAMP mutants. In fact, the Ras1-signaling pathway was found to be involved in osmotic and genotoxic stress response, and maintenance of cell wall integrity via the Cdc24-dependent signaling pathway. Through this microarray analysis, we have identified a number of cAMP-dependent genes, including GRE2, HSP12, ENA1, TCO2, PKP2, in C. neoformans. Most notably, we have found that the Ras/cAMP pathway promotes resistance to amphotericin B in C. neoformans, suggesting that an inhibitor(s) of the pathway should have a synergistic antifungal activity with the polyene drug. In conclusion, our study provides not only genome-wide comprehensive insights into pathogenomic SAS pathways in human fungal pathogens, but also unprecedented opportunity to develop a novel antifungal therapeutic method.