Assessing identity, redundancy and confounds in Gene Ontology annotations over time
Assessing identity, redundancy and confounds in Gene Ontology annotations over time
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DOI：
10.1093/bioinformatics/bts727
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发表时间：
2013-02-15
期刊：
影响因子：
5.8
通讯作者：
Pavlidis, Paul
中科院分区：
文献类型：
--
作者：
Gillis, Jesse;Pavlidis, Paul
动机：基因本体论（GO）是大量使用的系统生物学，但潜在的冗余，混淆与其他数据源和稳定性随时间推移的问题已经很少explored.Results：我们报告说，GO注释是稳定的，在短时间内，与3%的基因不是最语义相似的每月GO版本之间。然而，我们发现基因可以随着时间的推移改变它们的“功能身份”，两年后有20%的基因与自己不匹配（通过语义相似性）。我们进一步发现GO中的注释偏差，其中一些基因比其他基因更具特征，在酵母中有所下降，但在人类中普遍增加。最后，我们发现蛋白质相互作用数据库中的许多条目是由于用于GO注释的相同的已发表报告，66%的评估GO组表现出这种混淆。我们提供了一个案例研究，以说明如何使用这些信息的基因集和网络的分析。
Motivation: The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.Results: We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction data-bases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks.