PAP

PAP identifies potential transcriptional regulators and regulatory targets in mammalian genomes by analyzing promoters and characterized transcription factors to elucidate transcriptional regulatory mechanisms.

Key Features:

• Systematic Analysis: Considers all promoters and characterized transcription factors in its model to identify common regulators of co-expressed gene sets and genes regulated by specific TFs.
• Statistical Rigor: Implements a systematic statistical model and framework to assess significance of regulator–gene associations.
• Hypothesis Generation: Analyzes published and novel co-regulated gene sets to generate testable hypotheses about regulatory networks and pathways.
• Validation and Consistency: Predictions have been validated and shown to be consistent with experimental observations such as chromatin immunoprecipitation (ChIP) experiments.

Scientific Applications:

• Transcriptional regulator identification: Identify potential transcriptional regulators for sets of co-expressed genes.
• Regulatory target prediction: Pinpoint possible regulatory targets of transcription factors across the genome.
• Genetic network and pathway analysis: Dissect genetic networks underlying biological pathways and disease states using co-expression data from microarray studies.

Methodology:

Applies a systematic statistical model that evaluates promoters and characterized transcription factors genome-wide; the statistical framework has been validated against chromatin immunoprecipitation (ChIP) data and applied to co-expressed gene sets derived from microarray studies.