target

target implements and extends the BETA algorithm to infer direct target genes from DNA-binding and perturbation expression data and predict the combined function of two DNA-binding elements from comparable binding and expression data.

Key Features:

• BETA Algorithm Implementation: Implements the BETA algorithm from Wang et al. (2013) for inferring direct target genes from DNA-binding and perturbation expression data.
• Combined Function Prediction: Extends the BETA algorithm to predict the combined function of two DNA-binding elements from comparable binding and expression data.

Scientific Applications:

• Transcription Factor Target Identification: Identifies direct target genes of transcription factors using DNA-binding data (such as ChIP-seq) and gene expression perturbation data.
• Combined Transcription Factor Function Analysis: Predicts how pairs of DNA-binding elements or transcription factors function together to regulate gene expression.

Methodology:

The tool implements the BETA algorithm as described in Wang et al. (2013) with extensions for combined analysis of two DNA-binding elements.