Starr：Affyoung ChIP-chip数据的简单平铺阵列分析
Starr: Simple Tiling Array Analysis of Affymetrix ChIP-chip data
摘要：
染色质免疫沉淀结合DNA微阵列（ChIP芯片）是一种检测DNA-蛋白质结合或翻译后染色质/组蛋白修饰的方法。与所有高通量技术一样，它需要对数据进行彻底的生物信息学处理，目前还没有标准。主要目标是可靠地识别和定位结合特定蛋白质的基因组区域。第二步包括比较功能相关蛋白质的结合谱，或相同蛋白质在不同遗传背景或环境条件下的结合谱。最终，人们希望获得DNA结合事件对基因表达的影响的机制性理解。我们提出了一个免费的，开源的R包Starr，与Ringo包相结合，促进了跨实验和跨不同微阵列平台的ChIP芯片数据的比较分析。核心功能是数据导入、质量评估、数据的标准化和可视化，以及ChIP富集的基因组区域的检测。通用Bioconductor类的使用确保了与其他R包的兼容性。最重要的是，Starr提供了用于整合互补基因组学数据的方法，例如，它使得能够系统地研究基因表达和DNA结合之间的关系。
英文摘要：
Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay for DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires a thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is the reliable identification and localization of genomic regions that bind a specific protein. The second step comprises comparison of binding profiles of functionally related proteins, or of binding profiles of the same protein in different genetic backgrounds or environmental conditions. Ultimately, one would like to gain a mechanistic understanding of the effects of DNA binding events on gene expression. We present a free, open-source R package Starr that, in combination with the package Ringo, facilitates the comparative analysis of ChIP-chip data across experiments and across different microarray platforms. Core features are data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions. The use of common Bioconductor classes ensures the compatibility with other R packages. Most importantly, Starr provides methods for integration of complementary genomics data, e.g., it enables systematic investigation of the relation between gene expression and dna binding.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
