Performance Assessment of the Network Reconstruction Approaches on Various Interactomes
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2021.666705/full |
| _version_ | 1831590615575429120 |
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| author | M. Kaan Arici M. Kaan Arici Nurcan Tuncbag Nurcan Tuncbag |
| author_facet | M. Kaan Arici M. Kaan Arici Nurcan Tuncbag Nurcan Tuncbag |
| author_sort | M. Kaan Arici |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-18T01:08:08Z |
| format | Article |
| id | doaj.art-6c7ce5f4842f44dda97e64d428136da1 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-12-18T01:08:08Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-6c7ce5f4842f44dda97e64d428136da12022-12-21T21:26:11ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2021-10-01810.3389/fmolb.2021.666705666705Performance Assessment of the Network Reconstruction Approaches on Various InteractomesM. Kaan Arici0M. Kaan Arici1Nurcan Tuncbag2Nurcan Tuncbag3Graduate School of Informatics, Middle East Technical University, Ankara, TurkeyFoot and Mouth Diseases Institute, Ministry of Agriculture and Forestry, Ankara, TurkeyChemical and Biological Engineering, College of Engineering, Koc University, Istanbul, TurkeySchool of Medicine, Koc University, Istanbul, TurkeyBeyond 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.https://www.frontiersin.org/articles/10.3389/fmolb.2021.666705/fullprotein-protein interactionsinteractomenetwork reconstructionheat diffusionpersonalized PageRankprize-collecting Steiner forest |
| spellingShingle | M. Kaan Arici M. Kaan Arici Nurcan Tuncbag Nurcan Tuncbag Performance Assessment of the Network Reconstruction Approaches on Various Interactomes Frontiers in Molecular Biosciences protein-protein interactions interactome network reconstruction heat diffusion personalized PageRank prize-collecting Steiner forest |
| title | Performance Assessment of the Network Reconstruction Approaches on Various Interactomes |
| title_full | Performance Assessment of the Network Reconstruction Approaches on Various Interactomes |
| title_fullStr | Performance Assessment of the Network Reconstruction Approaches on Various Interactomes |
| title_full_unstemmed | Performance Assessment of the Network Reconstruction Approaches on Various Interactomes |
| title_short | Performance Assessment of the Network Reconstruction Approaches on Various Interactomes |
| title_sort | performance assessment of the network reconstruction approaches on various interactomes |
| topic | protein-protein interactions interactome network reconstruction heat diffusion personalized PageRank prize-collecting Steiner forest |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2021.666705/full |
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