Waardenberg Ashley J, Bassett Maya, Bouveret Romaric, Harvey Richard P
Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.
Present Address: Children's Medical Research Institute, Westmead, NSW, 2145, Australia.
BMC Bioinformatics. 2015 Sep 2;16:275. doi: 10.1186/s12859-015-0701-2.
Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention.
Herein, we present a bioinformatics tool, CompGO, for identifying Differentially Enriched Gene Ontologies, called DiEGOs, and pathways, through the use of a z-score derivation of log odds ratios, and visualizing these differences at GO and pathway level. Through public experimental data focused on the cardiac transcription factor NKX2-5, we illustrate the problems associated with comparing GO enrichments between experiments using a simple overlap approach.
We have developed an R/Bioconductor package, CompGO, which implements a new statistic normally used in epidemiological studies for performing comparative GO analyses and visualizing comparisons from . BED data containing genomic coordinates as well as gene lists as inputs. We justify the statistic through inclusion of experimental data and compare to the commonly used overlap method. CompGO is freely available as a R/Bioconductor package enabling easy integration into existing pipelines and is available at: http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.html.
基因本体论（GO）富集分析常用于从系统生物学实验中推断生物学意义。然而，确定DNA结合实验之间的差异GO和通路富集，或使用GO结构对实验进行分类，却很少受到关注。
在此，我们展示了一种生物信息学工具CompGO，它通过使用对数优势比的z分数推导来识别差异富集的基因本体（称为DiEGO）和通路，并在GO和通路水平上可视化这些差异。通过聚焦心脏转录因子NKX2-5的公共实验数据，我们阐述了使用简单重叠方法比较实验之间GO富集时存在的问题。
我们开发了一个R/Bioconductor软件包CompGO，它实现了一种通常用于流行病学研究的新统计方法，用于进行比较GO分析并可视化来自包含基因组坐标的.BED数据以及基因列表作为输入的比较。我们通过纳入实验数据来证明该统计方法的合理性，并与常用的重叠方法进行比较。CompGO作为一个R/Bioconductor软件包可免费获取，能够轻松集成到现有流程中，可在以下网址获取：http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.html 。
