• 中文核心期刊要目总览
  • 中国科技核心期刊
  • 中国科学引文数据库(CSCD)
  • 中国科技论文与引文数据库(CSTPCD)
  • 中国学术期刊文摘数据库(CSAD)
  • 中国学术期刊(网络版)(CNKI)
  • 中文科技期刊数据库
  • 万方数据知识服务平台
  • 中国超星期刊域出版平台
  • 国家科技学术期刊开放平台
  • 荷兰文摘与引文数据库(SCOPUS)
  • 日本科学技术振兴机构数据库(JST)
Yanfeng ZHANG, Bing SU. 2012: Peak identification for ChIP-seq data with no controls. 动物学研究, 33(E5-6): 121-128. DOI: 10.3724/SP.J.1141.2012.E05-06E121
引用本文: Yanfeng ZHANG, Bing SU. 2012: Peak identification for ChIP-seq data with no controls. 动物学研究, 33(E5-6): 121-128. DOI: 10.3724/SP.J.1141.2012.E05-06E121
Yanfeng ZHANG, Bing SU. 2012: Peak identification for ChIP-seq data with no controls. Zoological Research, 33(E5-6): 121-128. DOI: 10.3724/SP.J.1141.2012.E05-06E121
Citation: Yanfeng ZHANG, Bing SU. 2012: Peak identification for ChIP-seq data with no controls. Zoological Research, 33(E5-6): 121-128. DOI: 10.3724/SP.J.1141.2012.E05-06E121

Peak identification for ChIP-seq data with no controls

Peak identification for ChIP-seq data with no controls

  • 摘要: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is increasingly being used for genome-wide profiling of transcriptional regulation, as this technique enables dissection of the gene regulatory networks. With input as control, a variety of statistical methods have been proposed for identifying the enriched regions in the genome, i.e., the transcriptional factor binding sites and chromatin modifications. However, when there are no controls, whether peak calling is still reliable awaits systematic evaluations. To address this question, we used a Bayesian framework approach to show the effectiveness of peak calling without controls (PCWC). Using several different types of ChIP-seq data, we demonstrated the relatively high accuracy of PCWC with less than a 5% false discovery rate (FDR). Compared with previously published methods, e.g., the model-based analysis of ChIP-seq (MACS), PCWC is reliable with lower FDR. Furthermore, to interpret the biological significance of the called peaks, in combination with microarray gene expression data, gene ontology annotation and subsequent motif discovery, our results indicate PCWC possesses a high efficiency. Additionally, using in silico data, only a small number of peaks were identified, suggesting the significantly low FDR for PCWC.

     

    Abstract: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is increasingly being used for genome-wide profiling of transcriptional regulation, as this technique enables dissection of the gene regulatory networks. With input as control, a variety of statistical methods have been proposed for identifying the enriched regions in the genome, i.e., the transcriptional factor binding sites and chromatin modifications. However, when there are no controls, whether peak calling is still reliable awaits systematic evaluations. To address this question, we used a Bayesian framework approach to show the effectiveness of peak calling without controls (PCWC). Using several different types of ChIP-seq data, we demonstrated the relatively high accuracy of PCWC with less than a 5% false discovery rate (FDR). Compared with previously published methods, e.g., the model-based analysis of ChIP-seq (MACS), PCWC is reliable with lower FDR. Furthermore, to interpret the biological significance of the called peaks, in combination with microarray gene expression data, gene ontology annotation and subsequent motif discovery, our results indicate PCWC possesses a high efficiency. Additionally, using in silico data, only a small number of peaks were identified, suggesting the significantly low FDR for PCWC.

     

/

返回文章
返回