GeneNetworkBuilder

GeneNetworkBuilder discovers direct or indirect targets of transcription factors by generating regulatory networks from ChIP-chip or ChIP-seq data combined with microarray or RNA-seq gene expression data.

Key Features:

• Regulatory network generation: GeneNetworkBuilder generates a regulatory network of a transcription factor from a list of potential target genes derived from ChIP-chip or ChIP-seq data together with corresponding gene expression results.
• Multi-platform data integration: The package supports input from ChIP-chip, ChIP-seq, microarray, and RNA-seq technologies.

Scientific Applications:

• Transcription factor target identification: GeneNetworkBuilder enables discovery of direct or indirect targets of transcription factors through integrative analysis of binding and expression data.
• Gene regulatory network inference: The tool constructs regulatory networks linking transcription factors to their downstream target genes.

Methodology:

GeneNetworkBuilder inputs a list of genes of potential targets of one transcription factor from ChIP-chip or ChIP-seq, and the gene expression results, to generate a regulatory network of the transcription factor.