a4df68_2e8223af2701449182b8a5d1aa34ce72~mv2_d_5231_3511_s_4_2.jpg

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.

a4df68_4f438e2963ef47e4ae87a6c898f0f694~mv2.webp

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. 

a4df68_e033f8350f2648cab01b690109225501~mv2_d_4000_2250_s_2.webp

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.