TransFind

TransFind predicts transcription factor binding sites in promoter regions of co-regulated gene sets to infer transcription factors that drive gene expression changes and characterize transcriptional regulatory networks.

Key Features:

• Prediction of Transcription Factor Binding Sites: Identifies potential transcription factor binding sites within promoter regions of co-regulated gene sets.
• Integration with Phylogenetic Analysis: Incorporates phylogenetic conservation to prioritize binding site predictions across species.
• Multiple Testing Correction: Applies statistical methods to correct for multiple testing in prediction results.

Scientific Applications:

• Regulatory Network Characterization: Facilitates mapping of transcriptional regulatory networks by linking transcription factors to co-regulated gene sets.
• Gene Expression Studies: Enables inference of transcription factors that may drive observed gene expression changes across conditions.
• Evolutionary Biology: Supports analysis of evolutionary conservation of transcription factor binding sites using phylogenetic information.

Methodology:

Combines prediction of transcription factor binding sites with phylogenetic conservation analysis and statistical multiple-testing correction.