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Sengupta K, Saha S, Halder AK, Chatterjee P, Nasipuri M, Basu S, Plewczynski D. PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms. Front Genet 2022; 13:969915. [PMID: 36246645 PMCID: PMC9556876 DOI: 10.3389/fgene.2022.969915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Protein function prediction is gradually emerging as an essential field in biological and computational studies. Though the latter has clinched a significant footprint, it has been observed that the application of computational information gathered from multiple sources has more significant influence than the one derived from a single source. Considering this fact, a methodology, PFP-GO, is proposed where heterogeneous sources like Protein Sequence, Protein Domain, and Protein-Protein Interaction Network have been processed separately for ranking each individual functional GO term. Based on this ranking, GO terms are propagated to the target proteins. While Protein sequence enriches the sequence-based information, Protein Domain and Protein-Protein Interaction Networks embed structural/functional and topological based information, respectively, during the phase of GO ranking. Performance analysis of PFP-GO is also based on Precision, Recall, and F-Score. The same was found to perform reasonably better when compared to the other existing state-of-art. PFP-GO has achieved an overall Precision, Recall, and F-Score of 0.67, 0.58, and 0.62, respectively. Furthermore, we check some of the top-ranked GO terms predicted by PFP-GO through multilayer network propagation that affect the 3D structure of the genome. The complete source code of PFP-GO is freely available at https://sites.google.com/view/pfp-go/.
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Affiliation(s)
- Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Sovan Saha
- Department of Computer Science and Engineering, Institute of Engineering and Management, Kolkata, West Bengal, India
| | - Anup Kumar Halder
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Piyali Chatterjee
- Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata, India
| | - Mita Nasipuri
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
- *Correspondence: Subhadip Basu, Dariusz Plewczynski,
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- *Correspondence: Subhadip Basu, Dariusz Plewczynski,
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