Bhasin Jeffrey M, Ting Angela H
Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
Nucleic Acids Res. 2016 Jul 8;44(12):5550-6. doi: 10.1093/nar/gkw477. Epub 2016 Jun 1.
Bioinformatic analysis often produces large sets of genomic ranges that can be difficult to interpret in the absence of genomic context. Goldmine annotates genomic ranges from any source with gene model and feature contexts to facilitate global descriptions and candidate loci discovery. We demonstrate the value of genomic context by using Goldmine to elucidate context dynamics in transcription factor binding and to reveal differentially methylated regions (DMRs) with context-specific functional correlations. The open source R package and documentation for Goldmine are available at http://jeffbhasin.github.io/goldmine.
生物信息学分析常常会产生大量的基因组范围数据，在缺乏基因组背景信息的情况下，这些数据可能难以解读。Goldmine 用基因模型和特征背景注释来自任何来源的基因组范围，以促进全局描述和候选基因座的发现。我们通过使用 Goldmine 来阐明转录因子结合中的背景动态，并揭示具有背景特异性功能相关性的差异甲基化区域（DMR），从而证明了基因组背景的价值。Goldmine 的开源 R 包和文档可在 http://jeffbhasin.github.io/goldmine 获得。
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