Given the recent explosion of publications that employ microarray technology to monitor genome-wide expression and that correlate these expression changes to biological processes or to disease states, the determination of the transcriptional regulation of these co-expressed genes is the next major step toward deciphering the genetic network governing the pathway or disease under study. Although computational approaches have been proposed for this purpose, there is no integrated and user-friendly software application that allows experimental biologists to tackle this problem in higher eukaryotes.

Therefore, we have developed a systematic, statistical model of mammalian transcriptional regulatory sequence analysis, and we have created a comprehensive, user-friendly web application suite termed the Promoter Analysis Pipeline (PAP) to expose these features. PAP is suitable for the identification of the potential transcriptional regulators of co-expressed genes and the identification of the potential regulatory targets of transcription factors. A typical PAP analysis includes input of a co-expressed gene cluster, identification of several high scoring transcription factors and visualization of the predicted transcription factor binding sites. These functions allow biologists to predict transcriptional regulatory mechanisms of their genes under study.