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A computational pipeline that integrates data from GRO-seq, RNA-seq, histone modification ChIP-seq (i.e., H3K27ac and H3K4me1),and motif searches, allowing for the simultaneous identification of active enhancers and their cognate transcription factors across many samples.

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TFSEE integrates (1) the location and magnitude of enhancer activity based on enhancer transcription (GRO-seq); (2) the enrichment of enhancer-related histone modifications (ChIP-seq); (3) the level of TF expression (RNA-seq); (4) the level of target gene expression (RNA-seq); and (5) the TF motif scores for each enhancer. 

Total Functional Score of Enhancer Elements

TFSEE

groHMM

Figure from Chae M. et al. BMC Bioinformatics. 2015. 

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A computational tool for analyzing GRO-seq data and identifying unannotated and cell type-specific transcription units from global run-on sequencing data.

Homer

A software package for analyzing GRO-seq data and other types of NGS data sets such as RNA-seq and ChIP-seq.

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