Public Health Laboratory, Sulaimaniyah, Kurdistan Region, 46001, Iraq.
Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
BMC Bioinformatics. 2019 Jan 11;20(1):20. doi: 10.1186/s12859-018-2581-8.
Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up with different hypotheses and help further investigations of an experiment. The biological function for desired genes and gene associations is picked up from a randomly chosen list or through the analysis of differential gene expression. Many tools have been developed to utilize GO knowledge and cluster genes according to relevant biological functions. The retrieved GO terms include both specific and non-specific terms, which is not user-friendly in terms of data analysis. Thus one approach is still missing, which allows navigating through different levels of GO hierarchy manually.
We developed a tool, GOTrapper, which allows moving up or down to the very bottom of the GO hierarchy. This is performed manually by the user, based on an assigned threshold. This tool grabs the shared terms by the desired set of input genes of Homo sapiens. Here, two inputs are possible. "Within" is to find associated terms within one gene list, and "Between" is to find associated terms between two lists. The tool also provides the option to return the terms with the pre-selected evidence codes.
GOTrapper is a user-friendly Java tool that helps the user move up and down the ontology tree, which leads to new hypotheses and devising new association of the input genes. It also allows returning terms of associated genes based on selected evidence codes. This tool can be accessed and is freely available at https://github.com/BioGeneTools/GOTrapper .
基因本体论（GO）是一个有用的受控词汇资源，提供有关注释基因的信息。基于该资源，寻找生物功能对于生物学家提出不同的假设并帮助进一步研究实验非常有用。所需基因和基因关联的生物学功能是从随机选择的列表中提取的，或者通过分析差异基因表达来提取的。已经开发了许多工具来利用 GO 知识并根据相关的生物学功能对基因进行聚类。检索到的 GO 术语包括特定和非特定术语，这在数据分析方面不够用户友好。因此，仍然缺少一种方法，可以手动浏览 GO 层次结构的不同级别。
我们开发了一种工具 GOTrapper，它允许用户手动在 GO 层次结构中上下移动到最底层。这是根据用户分配的阈值来完成的。该工具抓取人类所需输入基因集的共享术语。在这里，有两种输入方式。“Within”用于在一个基因列表中查找相关术语，“Between”用于在两个列表之间查找相关术语。该工具还提供了返回预选证据代码的术语的选项。
GOTrapper 是一个用户友好的 Java 工具，可帮助用户在本体论树中上下移动，从而产生新的假设并设计输入基因的新关联。它还允许根据选定的证据代码返回相关基因的术语。该工具可在 https://github.com/BioGeneTools/GOTrapper 上访问和免费使用。
