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  A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

Rudolph, J. D., & Cox, J. (2019). A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. Journal of Proteome Research, 18(5), 2052-2064. doi:10.1021/acs.jproteome.8b00927.

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 Creators:
Rudolph, Jan Daniel1, Author              
Cox, Jürgen1, Author              
Affiliations:
1Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              

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Free keywords: PLATFORM; DATABASE; COMPLEXES; RESOURCEBiochemistry & Molecular Biology; computational proteomics; network analysis; Perseus;
 Abstract: Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affinity purification experiments, but networks are also used to explore proteomics data. PerseusNet supports the biomedical researcher for both modes of data analysis with a multitude of activities. For affinity purification, a volcano-plot-based statistical analysis method for network generation is featured which is scalable to large numbers of baits. For posttranslational modifications of proteins, such as phosphorylation, a collection of dedicated network analysis tools helps in elucidating cellular signaling events. Co-expression network analysis of proteomics data adopts established tools from transcriptome co-expression analysis. PerseusNet is extensible through a plugin architecture in a multi-lingual way, integrating analyses in C#, Python, and R, and is freely available at http://www.perseus-framework.org.

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Language(s): eng - English
 Dates: 2019
 Publication Status: Published in print
 Pages: 13
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

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Project name : -
Grant ID : 686547
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : GA ERC-2012-SyG_318987–ToPAG
Grant ID : 318987
Funding program : Funding Programme 7 (FP7)
Funding organization : European Commission (EC)

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Title: Journal of Proteome Research
  Other : J. Proteome Res.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 18 (5) Sequence Number: - Start / End Page: 2052 - 2064 Identifier: ISSN: 1535-3893
CoNE: https://pure.mpg.de/cone/journals/resource/111019664290000