GeneNetworkBuilder

GeneNetworkBuilder constructs regulatory networks by integrating ChIP-seq and ChIP-chip transcription factor binding data with microarray or RNA-seq expression profiles to identify and annotate direct and indirect TF targets.

Key Features:

• Integration of High-Throughput Data: Combines ChIP-seq and ChIP-chip data with microarray or RNA-seq expression datasets to link binding events with transcriptional outcomes.
• Identification of TF Binding Sites: Detects transcription factor (TF) binding sites from ChIP-seq and ChIP-chip datasets using advanced algorithms.
• Annotating Binding Sites: Annotates binding sites with relevant genomic information to provide biological context for each interaction.
• Integration with Gene Expression Data: Correlates TF binding data with gene expression profiles to distinguish direct versus indirect TF targets.
• Construction of Regulatory Networks: Constructs regulatory networks that represent interactions between TFs and their target genes inferred from binding and expression data.

Scientific Applications:

• Developmental Biology: Mapping TF regulatory networks to elucidate genetic control mechanisms underlying developmental processes.
• Environmental Response Studies: Characterizing how TF-mediated regulation changes in response to environmental perturbations.
• Disease Research: Identifying dysregulated transcriptional networks and candidate TF–target interactions associated with disease.

Methodology:

Identifies TF binding sites from ChIP-seq or ChIP-chip, annotates those sites with genomic information, and integrates them with microarray or RNA-seq expression data to construct regulatory networks.