GLAD4U: deriving and prioritizing gene lists from PubMed literature.
GLAD4U: deriving and prioritizing gene lists from PubMed literature.
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DOI：
10.1186/1471-2164-13-s8-s20
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Zhang B
中科院分区：
文献类型：
--
作者：
Jourquin J;Duncan D;Shi Z;Zhang B
回答诸如“哪些基因与乳腺癌有关？”通常需要通过PubMed搜索引擎检索相关出版物，阅读这些出版物，并创建基因列表。这一过程不仅耗时，而且容易出错。我们报告了GLAD4U(为您自动派生的基因列表)，这是一个新的、基于网络的免费基因检索和优先排序工具。GLAD4U利用NCBI的现有资源来确保计算效率。GLAD4U为三个基因本体论(GO)术语和三个疾病术语创建的基因列表的质量使用公共数据库中相应的“金标准”列表进行评估。对于所有的查询，GLAD4U基因列表显示出很高的召回率但准确率很低，导致F-度量很低。相比之下，EBIMed的召回率始终低于GLAD4U，但其准确率更高。为了在列表的顶端显示最相关的基因，我们研究了基于发表计数和超几何检验的两种排序方法，并将排序后的列表与EBIMed生成的列表与金标准进行了比较。在基于各种质量指标的所有查询中，这两种GLAD4U方法都优于EBIMed。此外，超几何方法通过对得分较低的基因进行阈值处理，可以获得更好的性能。此外，人工检查表明，许多假阳性可以用黄金标准的不完整性来解释。GLAD4U用户界面接受对PubMed的任何有效查询，其输出页面显示排序的基因列表和与每个基因相关的信息、按时间顺序排列的支持出版物、运行摘要以及用于文件导出、功能丰富和蛋白质相互作用网络分析的链接。GLAD4U的总体召回率很高。尽管精确度普遍较低，但优先排序方法成功地将真正相关的基因排在列表的顶部，以促进有效的浏览。GLAD4U使用简单，其接口位于：http://bioinfo.vanderbilt.edu/glad4u.
Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors. We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis. GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient browsing. GLAD4U is simple to use, and its interface can be found at: http://bioinfo.vanderbilt.edu/glad4u.