Integrating Networks and Proteomics: Moving Forward. Issue 12 (December 2016)

• Record Type: Journal Article
• Authors: Goh, Wilson Wen Bin; Wong, Limsoon
• Is Part Of: Trends in biotechnology. Volume 34:Issue 12(2016)
• Page Start: 951
• Page End: 959
• Publication Date: 2016-12
• Subjects: proteomics -- networks -- bioinformatics -- translational research.; Biotechnology -- Periodicals; Biochemical engineering -- Periodicals; Genetic engineering -- Periodicals; Industrial microbiology -- Periodicals; 660.605
• DOI: 10.1016/j.tibtech.2016.05.015
• Languages: English
• ISSNs: 0167-7799

Abstract

Abstract : Networks can resolve many analytical problems in proteomics, including incomplete coverage and inconsistency. Despite high expectations, network-related research in proteomics has experienced only modest growth. In practice, most current research examines non-quantitative usages, for example determining physical interactions among proteins or contextualizing a differential protein list, rather than addressing practical quantitative usages, for example predicting missing proteins or making sample-class predictions. Moreover, many applications are irreproducible and are not widely adopted owing to a lack of common standards, particularly evaluation criteria and gold-standard datasets. A concerted drive towards quantitative applications and convergence towards common standards is essential for 'network-based proteomics' to realize its development potential and make meaningful contributions to clinical applications. Trends: Network-based analysis based on protein complexes instead of full networks is a powerful new paradigm. Network-based proteomics will play an important role in quantitative functional analysis and will be integral in clinical diagnosis and drug development. Homogenizing benchmarks – both performance criteria and datasets (expression and reference networks) – is crucial for advancing network-based proteomics.