Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.
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DOI：
10.1021/ac901335x
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发表时间：
2009-12-01
影响因子：
7.4
通讯作者：
McComb, Mark E.
中科院分区：
文献类型：
--
作者：
Bhatia, Vivek N.;Perlman, David H.;Costello, Catherine E.;McComb, Mark E.
为了从蛋白质组学实验中获得生物学意义并建立可检验的假设，通过质谱或其他技术鉴定的蛋白质的分配必须补充额外的符号，例如已知蛋白质功能，蛋白质-蛋白质相互作用或生物学途径关联的信息。收集、组织和解释这些数据通常需要生物学研究领域的专家的投入，此外还需要从在线蛋白质数据库中耗时地搜索和汇编信息。此外，由于易于使用和免费提供的工具有限，因此将大量信息可视化可能具有挑战性。为了应对这些限制，我们已经着手设计软件，以自动注释和可视化的蛋白质组学数据，以加快研究的步伐。在这里，我们提出了研究蛋白质注释的软件工具（STRAP）-一个用户友好的开源C#应用程序。STRAP使用可免费访问的UniProtKB和EBI果阿数据库自动获取与蛋白质组学结果ID列表中的蛋白质相关的基因本体（GO）术语。STRAP以易于导航的表格格式进行总结，除了免费的GO术语外，还包含有关蛋白质的元信息。此外，用户可以编辑这些信息，以便将特定蛋白质的内部专业知识整合到更大的数据集中。STRAP为所有术语提供可排序的表格视图，以及饼图（生物过程，细胞组分和分子功能）和条形图（样本集的交叉比较）中GO术语关联数据的图形表示，以帮助解释大型数据集和差异分析实验。此外，感兴趣的蛋白质可以作为唯一的FASTA格式的文件导出，以允许质谱数据的可定制的重新搜索，并且与列表中的蛋白质对应的基因名称可以以Gaggle微格式编码，用于进一步表征，包括途径分析。STRAP教程和C#源代码可从http://cpctools.sourceforge.net免费获得。
In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP) – a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP includes meta-information on the protein in addition to complimentary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger dataset. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie (biological process, cellular component and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large datasets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry data, and gene names corresponding to the proteins in the lists may be encoded in the Gaggle microformat for further characterization, including pathway analysis. STRAP, a tutorial, and the C# source code are freely available from http://cpctools.sourceforge.net.
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影响因子：
3
作者：
Beisvag V;Jünge FK;Bergum H;Jølsum L;Lydersen S;Günther CC;Ramampiaro H;Langaas M;Sandvik AK;Laegreid A
通讯作者：
Laegreid A
通过分布式注释系统整合蛋白质注释资源。
影响因子：
14.9
作者：
Olason PI
通讯作者：
Olason PI
影响因子：
14.9
作者：
Reimand J;Kull M;Peterson H;Hansen J;Vilo J
通讯作者：
Vilo J
影响因子：
3
作者：
Bare JC;Shannon PT;Schmid AK;Baliga NS
通讯作者：
Baliga NS
影响因子：
4.4
作者：
McCarthy, Fiona M.;Wang, Nan;Magee, G. Bryce;Nanduri, Bindu;Lawrence, Mark L.;Camon, Evelyn B.;Barrell, Daniel G.;Hill, David P.;Dolan, Mary E.;Williams, W. Paul;Luthe, Dawn S.;Bridges, Susan M.;Burgess, Shane C.
通讯作者：
Burgess, Shane C.