Advances in high-throughput technologies such as ChIP-chip and the completion of human genomic sequences allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (ChIPModules) and a motif discovery approach (ChIPMotifs) to mine the ChIP-chip data. The ChIPModules approach begins with experimentally determined binding sites and integrates positional weight matrices, a comparative genomics approach, and statistical learning methods to identify transcriptional regulatory modules. Using E2F1 ChIP-chip data performed on ENCODE regions in both HeLa and MCF7 cells, we have identified five regulatory modules for E2F1. One of modules was validated by using ChIP-chip with arrays containing ~14,000 human promoters. The ChIPMotifs approach incorporates a bootstrap re-sampling method to statistically infer the optimal cutoff threshold for a position weight matrix (PWM) of a motif identified from ChIP-chip data by ab initio motif discovery programs. Using OCT4 ChIP-chip data, we developed an in vivo OCT4 PWM. We then used this PWM and our ChIPModules to identify transcription factors co-localizing with OCT4 in a testicular germ cell tumor (Ntera2 cells).