Goldmine integrates information placing genomic ranges into meaningful biological contexts
Goldmine integrates information placing genomic ranges into meaningful biological contexts
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DOI：
10.1093/nar/gkw477
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Ting, Angela H.
中科院分区：
文献类型：
--
作者：
Bhasin, Jeffrey M.;Ting, Angela H.
生物信息学分析通常产生大量的基因组范围，在缺乏基因组背景的情况下，这些范围可能难以解释。Goldmine使用基因模型和特征上下文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发现。我们证明了基因组上下文的价值，通过使用金矿阐明上下文动态转录因子结合，并揭示差异甲基化区域（DMR）与上下文特异性功能相关性。Goldmine的开源R包和文档可以在http://jeffbhasin.github.io/goldmine上找到。
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.