BioNAR: An Integrated Biological Network Analysis Package in Bioconductor
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Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.08.527636v1?rss=1

Authors: Mclean, C. D., Sorokin, A., Simpson, I., Armstrong, J. D., Sorokina, O.

Abstract: Biological function in protein complexes emerges from more than just the sum of their parts: molecules interact in a range of different subcomplexes and transfer signals/information around internal pathways. Modern proteomic techniques are excellent at producing a parts-list for such complexes, but more detailed analysis demands a network approach linking the molecules together and analyzing the emergent architectural properties. Methods developed for the analysis of networks in social sciences have proven very useful for splitting biological networks into communities leading to the discovery of sub-complexes enriched with molecules associated with specific diseases or molecular functions that are not apparent from the constituent components alone. Here we present the Bioconductor package BioNAR, which supports step-by-step analysis of biological/biomedical networks with the aim of quantifying and ranking each of the network's vertices based on network topology and clustering. Examples demonstrate that while BioNAR is not restricted to proteomic networks, it can predict a protein's impact within multiple complexes, and enables estimation of the co-occurrence of meta-data, i.e., diseases and functions across the network, identifying the clusters whose components are likely to share common function and mechanisms.

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