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Promoter Analysis WebTools Help

The Promoter Analysis Pipeline (PAP) has been developed to allow for the analysis of a set of coexpressed genes and the prediction of their transcriptional regulatory mechanisms. These coexpressed genes may be identified by mRNA expression profiling experiments, by a comprehensive understanding of genes involved in a biological pathway, or by known targets of a particular transcription factor. Using the hypothesis that these genes may be regulated by the same transcription factors, PAP searches all characterized transcription factor binding sites in their promoters and reports over-represented binding profiles. Furthermore, PAP is able to predict other genes in the genome that are likely to be regulated by the same set of transcription factors. These functionalities may be accessed through the web-based workbench or the provided application programming interface (API). In summary, PAP allows one to answer important biological questions such as:

What are the common transcriptional regulators of a set of coexpressed genes which are involved in the same biological process?
Which genes in the genome may be regulated by one or more transcriptional factors which are known to have important roles in a particular biological function?

PAP Workflow

This option allows you to download the PAP application programming interface. This interface allows communication between the PAP software and the application platform that you are using.

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. by Chang LW, Nagarajan R, Magee JA, Milbrandt J, Stormo GD.
Home | Microarray Data | Search | Software | Publications | Collaborative Projects
The Biomedical Informatics Core is a cooperative effort between the Siteman Cancer Center,
the Nagarajan Lab in the Department of Pathology and Immunology, and the Washington University Neuroscience Blueprint Core.