BETA is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor’s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor’s activating or repressive function.
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Wang, S., Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS.(2013)
Target analysis by integration of transcriptome and ChIP-seq data with BETA.
Nature protocols, 8(12), 2502-2515.