Klein Hans-Ulrich, Schäfer Martin
Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Boston, Massachusetts.
Harvard Medical School, Boston, Massachusetts.
Curr Protoc Hum Genet. 2016 Jul 1;90:20.3.1-20.3.16. doi: 10.1002/cphg.17.
The R package epigenomix has been designed to detect differentially transcribed gene isoforms that, in addition, exhibit altered histone modifications at their respective genomic loci. The package provides methods to map histone ChIP-seq profiles to isoforms and estimate their transcript abundances from RNA-seq data. Based on the differences observed between case and control samples in the RNA-seq and ChIP-seq data, a correlation measure is calculated for each isoform. The distribution of this correlation measure is further investigated by a Bayesian mixture model to (i) reveal the relationship between the studied histone modification and transcriptional activity, and (ii) detect specific isoforms with differences in both transcription values and histone modifications. The method is designed for experiments with a few or no replicates, and is superior to separate analyses of both data types in that setting. This unit illustrates the integrative analysis of ChIP-seq and RNA-seq data with epigenomix. © 2016 by John Wiley & Sons, Inc.
R软件包epigenomix旨在检测差异转录的基因异构体，这些异构体在其各自的基因组位点还表现出组蛋白修饰的改变。该软件包提供了将组蛋白ChIP-seq图谱映射到异构体并根据RNA-seq数据估计其转录本丰度的方法。基于RNA-seq和ChIP-seq数据中病例组和对照组样本之间观察到的差异，为每个异构体计算一个相关性度量。通过贝叶斯混合模型进一步研究这种相关性度量的分布，以（i）揭示所研究的组蛋白修饰与转录活性之间的关系，以及（ii）检测转录值和组蛋白修饰均存在差异的特定异构体。该方法专为少量或无重复的实验而设计，在该设置下优于对两种数据类型的单独分析。本单元说明了使用epigenomix对ChIP-seq和RNA-seq数据进行综合分析。© 2016约翰威立父子公司。
