HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes
A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of human protein complexes. Unfortunately, we still lack such a com...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-10-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022923001031 |
| _version_ | 1797281203410173952 |
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| author | Yuliang Pan Ruiyi Li Wengen Li Liuzhenghao Lv Jihong Guan Shuigeng Zhou |
| author_facet | Yuliang Pan Ruiyi Li Wengen Li Liuzhenghao Lv Jihong Guan Shuigeng Zhou |
| author_sort | Yuliang Pan |
| collection | DOAJ |
| description | A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of human protein complexes. Unfortunately, we still lack such a comprehensive atlas of experimentally validated protein complexes, which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes, as well as the underlying biological mechanisms. To fill this gap, we built Human Protein Complexes Atlas (HPC-Atlas), as far as we know, the most accurate and comprehensive atlas of human protein complexes available to date. We integrated two latest protein interaction networks, and developed a novel computational method to identify nearly 9000 protein complexes, including many previously uncharacterized complexes. Compared with the existing methods, our method achieved outstanding performance on both testing and independent datasets. Furthermore, with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-affected human protein complexes, and 456 multifunctional proteins that contain many potential moonlighting proteins. These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources, but also a valuable resource for exploring new biological findings. The HPC-Atlas webserver is freely available at http://www.yulpan.top/HPC-Atlas. |
| first_indexed | 2024-03-07T16:54:02Z |
| format | Article |
| id | doaj.art-942b7ed9205c46d0a208fbb78ab71599 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-07T16:54:02Z |
| publishDate | 2023-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-942b7ed9205c46d0a208fbb78ab715992024-03-03T04:29:20ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292023-10-01215976990HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein ComplexesYuliang Pan0Ruiyi Li1Wengen Li2Liuzhenghao Lv3Jihong Guan4Shuigeng Zhou5Department of Computer Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, ChinaTranslational Medical Center for Stem Cell Therapy, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200120, ChinaDepartment of Computer Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, ChinaDepartment of Computer Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, ChinaDepartment of Computer Science and Technology, College of Electronic and Information Engineering, Tongji University, Shanghai 201804, China; Corresponding authors.Shanghai Key Laboratory of Intelligent Information Processing, School of Computer Science, Fudan University, Shanghai 200433, China; Corresponding authors.A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells. For a complete understanding of human cellular functions, it is crucial to have a comprehensive atlas of human protein complexes. Unfortunately, we still lack such a comprehensive atlas of experimentally validated protein complexes, which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes, as well as the underlying biological mechanisms. To fill this gap, we built Human Protein Complexes Atlas (HPC-Atlas), as far as we know, the most accurate and comprehensive atlas of human protein complexes available to date. We integrated two latest protein interaction networks, and developed a novel computational method to identify nearly 9000 protein complexes, including many previously uncharacterized complexes. Compared with the existing methods, our method achieved outstanding performance on both testing and independent datasets. Furthermore, with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-affected human protein complexes, and 456 multifunctional proteins that contain many potential moonlighting proteins. These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources, but also a valuable resource for exploring new biological findings. The HPC-Atlas webserver is freely available at http://www.yulpan.top/HPC-Atlas.http://www.sciencedirect.com/science/article/pii/S1672022923001031Human protein complexProtein interaction networkSARS-CoV-2-affected complexMultifunctional proteinComplex identification method |
| spellingShingle | Yuliang Pan Ruiyi Li Wengen Li Liuzhenghao Lv Jihong Guan Shuigeng Zhou HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes Genomics, Proteomics & Bioinformatics Human protein complex Protein interaction network SARS-CoV-2-affected complex Multifunctional protein Complex identification method |
| title | HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes |
| title_full | HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes |
| title_fullStr | HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes |
| title_full_unstemmed | HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes |
| title_short | HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes |
| title_sort | hpc atlas computationally constructing a comprehensive atlas of human protein complexes |
| topic | Human protein complex Protein interaction network SARS-CoV-2-affected complex Multifunctional protein Complex identification method |
| url | http://www.sciencedirect.com/science/article/pii/S1672022923001031 |
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