README.md

Global Analysis of 500 enhancers in K562 cells with Mosaic-seq

Overview

This repository described our scripts and piplines for using Mosaic-seq to functionally evaluate enhancers in K562 cells. Through optimization of key parameters of Mosaic-seq, we demonstrate that both primary and secondary target genes can be identified in the assay. Our investigation of > 500 enhancers in K562 cells reveals an enhancer-centric, interwoven regulatory network that converges to reguate the same sub-modules.

Requirement

• Numpy
• Scipy
• Pandas
• Matplotlib
• GSEApy
• NetworkX
• Force Atlas 2
• Bezier for NetworkX

File Organization

Original Fastq Files

GEO accession: GSE129837

Notebooks (In developemnt)

• Hits Identification

  • Plotting Primary and Secondary Hits

• Network Analysis

  • Network Analysis

• Downstream Analysis

  • GSEA Analysis
  • GWAS Hits Filtering

Contributors

• First Author: Russell Xie [email protected]
• Corresponding Author: Gary Hon [email protected]

How to cite

Xie S, Armendariz D, Zhou P, Duan J, Hon GC^*. Global analysis of enhancer targets reveals convergent enhancer-driven regulatory modules. Cell Reports. 29, 2570–2578.e5 2019 Link to paper