Arighi Cecilia N, Siu Amy Y, Tudor Catalina O, Nchoutmboube Jules A, Wu Cathy H, Shanker Vijay K
Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA.
Methods Mol Biol. 2011;694:63-75. doi: 10.1007/978-1-60761-977-2_5.
Technologies and experimental strategies have improved dramatically in the field of genomics and proteomics facilitating analysis of cellular and biochemical processes, as well as of proteins networks. Based on numerous such analyses, there has been a significant increase of publications in life sciences and biomedicine. In this respect, knowledge bases are struggling to cope with the literature volume and they may not be able to capture in detail certain aspects of proteins and genes. One important aspect of proteins is their phosphorylated states and their implication in protein function and protein interacting networks. For this reason, we developed eFIP, a web-based tool, which aids scientists to find quickly abstracts mentioning phosphorylation of a given protein (including site and kinase), coupled with mentions of interactions and functional aspects of the protein. eFIP combines information provided by applications such as eGRAB, RLIMS-P, eGIFT and AIIAGMT, to rank abstracts mentioning phosphorylation, and to display the results in a highlighted and tabular format for a quick inspection. In this chapter, we present a case study of results returned by eFIP for the protein BAD, which is a key regulator of apoptosis that is posttranslationally modified by phosphorylation.
在基因组学和蛋白质组学领域,技术和实验策略有了显著改进,这有助于分析细胞和生化过程以及蛋白质网络。基于众多此类分析,生命科学和生物医学领域的出版物数量大幅增加。在这方面,知识库难以应对如此庞大的文献量,可能无法详细捕捉蛋白质和基因的某些方面。蛋白质的一个重要方面是其磷酸化状态及其在蛋白质功能和蛋白质相互作用网络中的作用。因此,我们开发了eFIP,这是一个基于网络的工具,可帮助科学家快速找到提及特定蛋白质磷酸化(包括位点和激酶)的摘要,以及提及该蛋白质相互作用和功能方面的内容。eFIP整合了eGRAB、RLIMS-P、eGIFT和AIIAGMT等应用程序提供的信息,对提及磷酸化的摘要进行排名,并以突出显示的表格形式展示结果,以便快速查看。在本章中,我们展示了eFIP针对蛋白质BAD返回结果的案例研究,BAD是细胞凋亡的关键调节因子,可通过磷酸化进行翻译后修饰。
Methods Mol Biol. 2011
Database (Oxford). 2012-12-5
Database (Oxford). 2014-8-13
BMC Bioinformatics. 2010-8-9
Bioinformatics. 2006-7-1
Nucleic Acids Res. 2018-1-4
IEEE/ACM Trans Comput Biol Bioinform. 2015
IEEE/ACM Trans Comput Biol Bioinform. 2011-4-27
Mol Cell Proteomics. 2022-12
Database (Oxford). 2014-8-13
BMC Bioinformatics. 2013-3-22
Database (Oxford). 2012-12-5
BMC Bioinformatics. 2009-7-17
Genome Biol. 2008
Bioinformatics. 2008-7-1
Nucleic Acids Res. 2008-7-1
Nucleic Acids Res. 2008-7-1