Common microarray and next-generation sequencing data analysis concentrate on tumor subtype classification,marker detection,\r\nand transcriptional regulation discovery during biological processes by exploring the correlated gene expression patterns and their\r\nshared functions. Genetic regulatory network (GRN) based approaches have been employed in many large studies in order to\r\nscrutinize for dysregulation and potential treatment controls. In addition to gene regulation and network construction, the concept\r\nof the network modulator that has significant systemic impact has been proposed, and detection algorithms have been developed\r\nin past years. Here we provide a unified mathematic description of these methods, followed with a brief survey of these modulator\r\nidentification algorithms. As an early attempt to extend the concept to new RNA regulation mechanism, competitive endogenous\r\nRNA (ceRNA), into amodulator framework, we provide two applications to illustrate the network construction,modulation effect,\r\nand the preliminary finding from these networks. Those methods we surveyed and developed are used to dissect the regulated\r\nnetwork under different modulators. Not limit to these, the concept of ââ?¬Å?modulationââ?¬Â can adapt to various biological mechanisms\r\nto discover the novel gene regulation mechanisms.
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