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Extending protein interaction networks using proteoforms and small molecules

Hernandez Sanchez, L. F.; Burger, B.; Castro Campos, R. A.; Johansson, S.; Njolstad, P. R.; Barsnes, H.; Vaudel, M.

2022-09-07 bioinformatics
10.1101/2022.09.06.506730 bioRxiv
Show abstract

Biological network analysis is used to interpret modern high-throughput biomedical data sets in terms of biological functions and pathways. However, the results greatly depend on the topological characteristics of the underlying network, commonly composed of nodes representing genes or proteins that are connected by edges when interacting. In this study, we build biological networks accounting for small molecules, protein isoforms and post-translational modifications. We highlight how these change the global structure of the network and how the connectedness of pathway-based networks is altered. Our findings highlight the importance of carefully crafting the networks for network analysis to better represent the reality of biological systems.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.