ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach.
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach.
复制标题
ChIP-BIT2：一个使用贝叶斯集成方法检测弱绑定事件的软件工具。
DOI：
10.1186/s12859-021-04108-5
复制
发表时间：
2021-04-15
影响因子：
3
通讯作者：
Xuan J
中科院分区：
文献类型：
--
作者：
Chen X;Shi X;Neuwald AF;Hilakivi-Clarke L;Clarke R;Xuan J
CHIP-SEQ将染色质免疫沉淀分析与测序相结合，识别DNA结合蛋白的全基因组结合位点。虽然许多结合位点有很强的CHIP-SEQ‘峰’观察，并被很好地捕获，但仍然有一些区域与蛋白质结合较弱，具有相对较低的CHIP-SEQ信号浓缩。这些弱结合位点，特别是启动子和增强子上的结合位点，功能上很重要，因为它们也调节附近的基因表达。然而，由于从扩增的背景DNA中区分这些弱结合位点的模糊性，准确地识别芯片序列数据中的弱结合位点仍然是一个挑战。CHIP-BIT2(http://sourceforge.net/projects/chipbitc/)是用于CHIP-SEQ峰值检测的软件包。CHIP-BIT2采用一种结合蛋白质和对照CHIP-SEQ数据的混合模型，并预测启动子、增强子或其他基因组位置上的强或弱蛋白质结合位点。对于基因启动子的结合位点，CHIP-BIT2同时预测它们的目标基因。CHIP-BIT2已经在基准区域上进行了验证，并使用大规模的ENCODE CHIP-SEQ数据进行了测试，证明了其高精度和广泛的适用性。CHIP-BIT2是一种高效的CHIP-SEQ峰值呼叫器。它提供了一个更好的透镜来检测弱结合位点，并可以精炼或扩展现有的结合位点集合，为解码基因表达调控的机制提供额外的调节区。网上版载有补充材料，可在10.1186/s12859-021-04108-5查阅。
ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs. ChIP-BIT2 (http://sourceforge.net/projects/chipbitc/) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability. ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation. The online version contains supplementary material available at 10.1186/s12859-021-04108-5.
登录
查看更多内容
影响因子：
5.8
作者：
Chen, Xi;Gu, Jinghua;Xuan, Jianhua
通讯作者：
Xuan, Jianhua
影响因子：
4.6
作者：
Chen, Xi;Gu, Jinghua;Xuan, Jianhua
通讯作者：
Xuan, Jianhua
DOI：
10.1073/pnas.1813565116
发表时间：
2019-02-26
影响因子：
11.1
作者：
Ngo, Vu;Chen, Zhao;Wang, Wei
通讯作者：
Wang, Wei
影响因子：
16.6
作者：
Mercado, Nicolas;Schutzius, Gabi;Kirkland, Susan
通讯作者：
Kirkland, Susan
影响因子：
64.8
作者：
Visel, Axel;Blow, Matthew J.;Li, Zirong;Zhang, Tao;Akiyama, Jennifer A.;Holt, Amy;Plajzer-Frick, Ingrid;Shoukry, Malak;Wright, Crystal;Chen, Feng;Afzal, Veena;Ren, Bing;Rubin, Edward M.;Pennacchio, Len A.
通讯作者：
Pennacchio, Len A.