The role of Yamanaka factors as the core regulators in the induction of pluripotency during somatic cell reprogramming has been discovered recently. Our previous study found that Yamanaka factors regulate a developmental signaling network in maintaining embryonic stem (ES) cell pluripotency. Here, we established completely reprogrammed induced pluripotent stem (iPS) cells and analyzed the global promoter occupancy of Yamanaka factors in these cells by ChIP-chip assays. We found that promoters of 565 genes were co-bound by four Yamanaka factors in iPS cells, a 10-fold increase when compared with their binding in ES cells. The promoters occupied by a single Yamanaka factor distributed equally in activated and repressed genes in iPS cells, while in ES cells Oct4, Sox2, or Klf4 distributed mostly in repressed genes and c-Myc in activated ones. Pathway analysis of the ChIP-chip data revealed that Yamanaka factors regulated 16 developmental signaling pathways in iPS cells, among which 12 were common and 4 were unique compared to pathways regulated in ES cells. We further analyzed another recently published ChIP-chip dataset in iPS cells and observed similar results, showing the power of ChIP-chip plus pathway analysis for revealing the nature of pluripotency maintenance and regeneration. Next, we experimentally tested one of the repressive signaling pathways and found that its inhibition indeed improved efficiency of cell reprogramming. Taken together, we proposed that there is a core developmental signaling network necessary for pluripotency, with TGF-beta, Hedgehog, Wnt, p53 as repressive (Yin) regulators and Jak-STAT, cell cycle, focal adhesion, adherens junction as active (Yang) ones; and Yamanaka factors synergistically regulate them in a Yin-Yang balanced way to induce pluripotency.