Optimized Protein–Protein Interaction Network Usage with Context Filtering

  • Natalia Pietrosemoli
  • Maria Pamela DobayEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1819)


Protein–protein interaction networks (PPIs) collect information on physical—and in some cases–functional interactions between proteins. Most PPIs are annotated with confidence scores, which reflect the probability that a reported interaction is a true interaction. These scores, however, do not allow users to isolate interactions relevant in a particular biological context. Here, we describe solutions for performing context filtering on PPIs to allow biological data interpretation and functional inference in two publicly available PPIs resources (HIPPIE and STRING) and in the proprietary pathway analysis tool and knowledge base Ingenuity Pathway Analysis.

Key words

Protein–protein interaction networks Context filtering Orthogonal text mining resources 



This work was supported by the Swiss Initiative in Systems Biology, SystemsX, through a fellowship (2013/137) provided to M.P.D.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 CNRSParisFrance
  2. 2.SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment GénopodeLausanneSwitzerland
  3. 3.IQVIABaselSwitzerland
  4. 4.Yocto Group LimitedZurichSwitzerland

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