ABSTRACT
This chapter reviews how the Cap Analysis of Gene Expression (CAGE) data can be integrated with other measurements such as expression, physical interactions and computational prediction of regulatory motifs, which together can provide a genome-wide picture of eukaryotic transcriptional regulatory networks at a new level of resolution. From a global point of view, one can consider the plethora of interacting molecules as a network of molecular entities that dynamically form under specific intra- and extra-cellular demands and execute their programmed actions accordingly. CAGE expression and mapping data are integrated with other expression data in order to infer all transcription factors and the regulated genes which are expressed by the system, representing the nodes of the network. Although CAGE provides for digital counting of gene expression, expression profiling using micro-array chips is by far the most popular genome-wide technology for capturing genomic reaction of a cell.
