Performance Assessment of the Network Reconstruction Approaches on Various Interactomes

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2021-10-01

Author

Arici, M. Kaan
Tunçbağ, Nurcan

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Beyond the list of molecules, there is a necessity to collectively consider multiple sets of omic data and to reconstruct the connections between the molecules. Especially, pathway reconstruction is crucial to understanding disease biology because abnormal cellular signaling may be pathological. The main challenge is how to integrate the data together in an accurate way. In this study, we aim to comparatively analyze the performance of a set of network reconstruction algorithms on multiple reference interactomes. We first explored several human protein interactomes, including PathwayCommons, OmniPath, HIPPIE, iRefWeb, STRING, and ConsensusPathDB. The comparison is based on the coverage of each interactome in terms of cancer driver proteins, structural information of protein interactions, and the bias toward well-studied proteins. We next used these interactomes to evaluate the performance of network reconstruction algorithms including all-pair shortest path, heat diffusion with flux, personalized PageRank with flux, and prize-collecting Steiner forest (PCSF) approaches. Each approach has its own merits and weaknesses. Among them, PCSF had the most balanced performance in terms of precision and recall scores when 28 pathways from NetPath were reconstructed using the listed algorithms. Additionally, the reference interactome affects the performance of the network reconstruction approaches. The coverage and disease- or tissue-specificity of each interactome may vary, which may result in differences in the reconstructed networks.

Subject Keywords

Protein-protein interactions, Interactome, Network reconstruction, Heat diffusion, Personalized PageRank, Prize-collecting Steiner forest, Pathway reconstruction

URI

https://hdl.handle.net/11511/94310

Journal

FRONTIERS IN MOLECULAR BIOSCIENCES

DOI

https://doi.org/10.3389/fmolb.2021.666705

Collections

Graduate School of Informatics, Article

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Citation Formats

M. K. Arici and N. Tunçbağ, “Performance Assessment of the Network Reconstruction Approaches on Various Interactomes,” FRONTIERS IN MOLECULAR BIOSCIENCES, vol. 8, pp. 0–0, 2021, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/94310.