An interactive environment for agile analysis and visualization of ChIP-sequencing data

TY - JOUR

T1 - An interactive environment for agile analysis and visualization of ChIP-sequencing data

AU - Lerdrup, Mads

AU - Johansen, Jens Vilstrup

AU - Agrawal-Singh, Shuchi

AU - Hansen, Klaus

PY - 2016/4/5

Y1 - 2016/4/5

N2 - To empower experimentalists with a means for fast and comprehensive chromatin immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated computational environment, EaSeq. The software combines the exploratory power of genome browsers with an extensive set of interactive and user-friendly tools for genome-wide abstraction and visualization. It enables experimentalists to easily extract information and generate hypotheses from their own data and public genome-wide datasets. For demonstration purposes, we performed meta-analyses of public Polycomb ChIP-seq data and established a new screening approach to analyze more than 900 datasets from mouse embryonic stem cells for factors potentially associated with Polycomb recruitment. EaSeq, which is freely available and works on a standard personal computer, can substantially increase the throughput of many analysis workflows, facilitate transparency and reproducibility by automatically documenting and organizing analyses, and enable a broader group of scientists to gain insights from ChIP-seq data.

AB - To empower experimentalists with a means for fast and comprehensive chromatin immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated computational environment, EaSeq. The software combines the exploratory power of genome browsers with an extensive set of interactive and user-friendly tools for genome-wide abstraction and visualization. It enables experimentalists to easily extract information and generate hypotheses from their own data and public genome-wide datasets. For demonstration purposes, we performed meta-analyses of public Polycomb ChIP-seq data and established a new screening approach to analyze more than 900 datasets from mouse embryonic stem cells for factors potentially associated with Polycomb recruitment. EaSeq, which is freely available and works on a standard personal computer, can substantially increase the throughput of many analysis workflows, facilitate transparency and reproducibility by automatically documenting and organizing analyses, and enable a broader group of scientists to gain insights from ChIP-seq data.

KW - Animals

KW - Chromatin Immunoprecipitation

KW - Genome

KW - Mice

KW - Polycomb-Group Proteins

KW - Software

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1038/nsmb.3180

DO - 10.1038/nsmb.3180

M3 - Journal article

C2 - 26926434

SN - 1545-9993

VL - 23

SP - 349

EP - 357

JO - Nature Structural and Molecular Biology

JF - Nature Structural and Molecular Biology

IS - 4

ER -