Iaseq: integrative analysis of allele-specificity of protein-dna interactions in multiple chip-seq datasets
文献类型：期刊论文
| 作者 | Wei,Yingying1; Li,Xia2,3; Wang,Qian-fei2; Ji,Hongkai1 |
| 刊名 | Bmc genomics
 |
| 出版日期 | 2012-11-29 |
| 卷号 | 13期号:1 |
| 关键词 | Allele-specific binding Transcription factor Histone modification Data integration Next-generation sequencing Statistical model |
| ISSN号 | 1471-2164 |
| DOI | 10.1186/1471-2164-13-681 |
| 通讯作者 | Ji,hongkai(hji@jhsph.edu) |
| 英文摘要 | Abstractbackgroundchip-seq provides new opportunities to study allele-specific protein-dna binding (asb). however, detecting allelic imbalance from a single chip-seq dataset often has low statistical power since only sequence reads mapped to heterozygote snps are informative for discriminating two alleles.resultswe develop a new method iaseq to address this issue by jointly analyzing multiple chip-seq datasets. iaseq uses a bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. using the discovered correlation patterns, the model allows one to borrow information across datasets to improve detection of allelic imbalance. application of iaseq to 77 chip-seq samples from 40 encode datasets and 1 genomic dna sample in gm12878 cells reveals that allele-specificity of multiple proteins are highly correlated, and demonstrates the ability of iaseq to improve allelic inference compared to analyzing each individual dataset separately.conclusionsiaseq illustrates the value of integrating multiple datasets in the allele-specificity inference and offers a new tool to better analyze asb. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/1471-2164-13-681 |
| 出版者 | BioMed Central |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2374294 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Ji,Hongkai |
| 作者单位 | 1.Johns Hopkins University Bloomberg School of Public Health; Department of Biostatistics 2.Chinese Academy of Sciences; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics 3.University of Chinese Academy of Sciences |
| 推荐引用方式 GB/T 7714 | Wei,Yingying,Li,Xia,Wang,Qian-fei,et al. Iaseq: integrative analysis of allele-specificity of protein-dna interactions in multiple chip-seq datasets[J]. Bmc genomics,2012,13(1). |
| APA | Wei,Yingying,Li,Xia,Wang,Qian-fei,&Ji,Hongkai.(2012).Iaseq: integrative analysis of allele-specificity of protein-dna interactions in multiple chip-seq datasets.Bmc genomics,13(1). |
| MLA | Wei,Yingying,et al."Iaseq: integrative analysis of allele-specificity of protein-dna interactions in multiple chip-seq datasets".Bmc genomics 13.1(2012). |
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来源：中国科学院大学
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