Computational pipeline for analysis of biomedical networks with BioNAR

Colin McLean, Anatoly Sorokin, James Douglas Armstrong, Oksana Sorokina*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

In a living cell, proteins interact to assemble both transient and constant molecular complexes, which transfer signals/information around internal pathways. Modern proteomic techniques can identify the constituent components of these complexes, but more detailed analysis demands a network approach linking the molecules together and analyzing the emergent architectural properties. The Bioconductor package BioNAR combines a selection of existing R protocols for network analysis with newly designed original methodological features to support step-by-step analysis of biological/biomedical . Critically, BioNAR supports a pipeline approach whereby many networks and iterative analyses can be performed. Here we present a network analysis pipeline that starts from initiating a network model from a list of components/proteins and their interactions through to identifying its functional components based solely on network topology. We demonstrate that BioNAR can help users achieve a number of network analysis goals that are difficult to achieve anywhere else. This includes how users can choose the optimal clustering algorithm from a range of options based on independent annotation enrichment, and predict a protein's influence within and across multiple subcomplexes in the network and estimate the co-occurrence or linkage between metadata at the network level (e.g., diseases and functions across the network, identifying the clusters whose components are likely to share common function and mechanisms). The package is freely available in Bioconductor release 3.17: https://bioconductor.org/packages/3.17/bioc/html/BioNAR.html. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Creating and annotating the network

Support Protocol 1: Installing BioNAR from RStudio

Support Protocol 2: Building the sample network from synaptome.db

Basic Protocol 2: Network properties and centrality

Basic Protocol 3: Network communities

Basic protocol 4: Choosing the optimal clustering algorithm based on the enrichment with annotation terms

Basic Protocol 5: Influencing network components and bridgeness

Basic Protocol 6: Co-occurrence of the annotations
Original languageEnglish
Article numbere940
Pages (from-to)1-31
Number of pages31
JournalCurrent Protocols
Volume3
Issue number12
DOIs
Publication statusPublished - 4 Dec 2023

Keywords / Materials (for Non-textual outputs)

  • network analysis
  • protein-protein interaction network
  • clustering

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