Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data.

IF 6.1 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Molecular & Cellular Proteomics Pub Date : 2025-03-13 DOI:10.1016/j.mcpro.2025.100947

Dušica Vidović, Behrouz Shamsaei, Stephan C Schürer, Phillip Kogan, Szymon Chojnacki, Michal Kouril, Mario Medvedovic, Wen Niu, Evren U Azeloglu, Marc R Birtwistle, Yibang Chen, Tong Chen, Jens Hansen, Bin Hu, Ravi Iyengar, Gomathi Jayaraman, Hong Li, Tong Liu, Eric A Sobie, Yuguang Xiong, Matthew J Berberich, Gary Bradshaw, Mirra Chung, Robert A Everley, Ben Gaudio, Marc Hafner, Marian Kalocsay, Caitlin E Mills, Maulik K Nariya, Peter K Sorger, Kartik Subramanian, Chiara Victor, Maria Banuelos, Victoria Dardov, Ronald Holewinski, Danica-Mae Manalo, Berhan Mandefro, Andrea D Matlock, Loren Ornelas, Dhruv Sareen, Clive N Svendsen, Vineet Vaibhav, Jennifer E Van Eyk, Vidya Venkatraman, Steve Finkbiener, Ernest Fraenkel, Jeffrey Rothstein, Leslie Thompson, Jacob Asiedu, Steven A Carr, Karen E Christianson, Desiree Davison, Deborah O Dele-Oni, Katherine C DeRuff, Shawn B Egri, Alvaro Sebastian Vaca Jacome, Jacob D Jaffe, Daniel Lam, Lev Litichevskiy, Xiaodong Lu, James Mullahoo, Adam Officer, Malvina Papanastasiou, Ryan Peckner, Caidin Toder, Joel Blanchard, Michael Bula, Tak Ko, Li-Huei Tsai, Jennie Z Young, Vagisha Sharma, Ajay Pillai, Jarek Meller, Michael J MacCoss

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引用次数: 0

Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.

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来源期刊

Molecular & Cellular Proteomics 生物-生化研究方法

CiteScore

11.50

自引率

4.30%

发文量

131

审稿时长

84 days

期刊介绍： The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action. The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data. Scope: -Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights -Novel experimental and computational technologies -Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes -Pathway and network analyses of signaling that focus on the roles of post-translational modifications -Studies of proteome dynamics and quality controls, and their roles in disease -Studies of evolutionary processes effecting proteome dynamics, quality and regulation -Chemical proteomics, including mechanisms of drug action -Proteomics of the immune system and antigen presentation/recognition -Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease -Clinical and translational studies of human diseases -Metabolomics to understand functional connections between genes, proteins and phenotypes