Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining

Kun Hsing Yu, Tsung Lu Michael Lee, Chi Shiang Wang, Yu Ju Chen, Christopher Ré, Samuel C. Kou, Jung-Hsien Chiang, Isaac S. Kohane, Michael Snyder

研究成果: Article同行評審

14 引文 斯高帕斯(Scopus)

摘要

There are more than 3.7 million published articles on the biological functions or disease implications of proteins, constituting an important resource of proteomics knowledge. However, it is difficult to summarize the millions of proteomics findings in the literature manually and quantify their relevance to the biology and diseases of interest. We developed a fully automated bioinformatics framework to identify and prioritize proteins associated with any biological entity. We used the 22 targeted areas of the Biology/Disease-driven (B/D)-Human Proteome Project (HPP) as examples, prioritized the relevant proteins through their Protein Universal Reference Publication-Originated Search Engine (PURPOSE) scores, validated the relevance of the score by comparing the protein prioritization results with a curated database, computed the scores of proteins across the topics of B/D-HPP, and characterized the top proteins in the common model organisms. We further extended the bioinformatics workflow to identify the relevant proteins in all organ systems and human diseases and deployed a cloud-based tool to prioritize proteins related to any custom search terms in real time. Our tool can facilitate the prioritization of proteins for any organ system or disease of interest and can contribute to the development of targeted proteomic studies for precision medicine.

原文English
頁(從 - 到)1383-1396
頁數14
期刊Journal of Proteome Research
17
發行號4
DOIs
出版狀態Published - 2018 四月 6

All Science Journal Classification (ASJC) codes

  • 生物化學
  • 化學 (全部)

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