In spite of the close relationship between phosphorylation and transcriptional regulation, the two networks are generally investigated separately. Many experimental and computational approaches endeavor to disclose the pair-wise interactions of both networks [1] [2] [6] [7] [8] [9] [10]. However, integrative studies of the two networks are very limited. A recent study generated a first-generation phosphorylation map for S.cerevisiae, and integrated the phosphorylation results with transcription factor binding **data** [1]. The results demonstrated that the largest class of kinase substrate is transcription factors, and revealed several new regulatory modules. Another study demonstrated in the cell cycle process, cyclin-dependent protein kinase (CDK) and transcription factors commonly form feed forward loops to activate different phases of the cell cycle [11]. In these studies, kinase/phosphatase and transcription factor are connected via biochemical interactions. Although such approaches have shed light on the prevalent regulatory motifs in the signaling network, the functional link between these regulators cannot be inferred. In this study, we propose to link kinase/phosphatase and transcription factor by using the transcriptome as an anchor.