Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network
Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs) is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when a...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-06-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1687157X17301117 |
| _version_ | 1797203867828486144 |
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| author | Pooja Sharma D.K. Bhattacharyya J.K. Kalita |
| author_facet | Pooja Sharma D.K. Bhattacharyya J.K. Kalita |
| author_sort | Pooja Sharma |
| collection | DOAJ |
| description | Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs) is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called CSC to detect protein complexes. The method is evaluated in terms of positive predictive value, sensitivity and accuracy using the datasets of the model organism, yeast and humans. CSC outperforms several other competing algorithms for both organisms. Further, we present a framework to establish the usefulness of CSC in analyzing the influence of a given disease gene in a complex topologically as well as biologically considering eight major association factors. Keywords: Protein complex, Connectivity, Semantic similarity, Contribution |
| first_indexed | 2024-04-24T08:26:10Z |
| format | Article |
| id | doaj.art-b3f7e03bd65041d9b8ce6f9af14ac52a |
| institution | Directory Open Access Journal |
| issn | 1687-157X |
| language | English |
| last_indexed | 2024-04-24T08:26:10Z |
| publishDate | 2018-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-b3f7e03bd65041d9b8ce6f9af14ac52a2024-04-16T22:47:51ZengElsevierJournal of Genetic Engineering and Biotechnology1687-157X2018-06-01161217226Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction networkPooja Sharma0D.K. Bhattacharyya1J.K. Kalita2Department of Computer Science & Engineering, Tezpur University Napaam, Tezpur 784028, Assam, IndiaDepartment of Computer Science & Engineering, Tezpur University Napaam, Tezpur 784028, Assam, India; Corresponding author.Department of Computer Science, University of Colorado at Colorado, Springs, CO 80933-7150, USAProtein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs) is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called CSC to detect protein complexes. The method is evaluated in terms of positive predictive value, sensitivity and accuracy using the datasets of the model organism, yeast and humans. CSC outperforms several other competing algorithms for both organisms. Further, we present a framework to establish the usefulness of CSC in analyzing the influence of a given disease gene in a complex topologically as well as biologically considering eight major association factors. Keywords: Protein complex, Connectivity, Semantic similarity, Contributionhttp://www.sciencedirect.com/science/article/pii/S1687157X17301117 |
| spellingShingle | Pooja Sharma D.K. Bhattacharyya J.K. Kalita Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network Journal of Genetic Engineering and Biotechnology |
| title | Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network |
| title_full | Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network |
| title_fullStr | Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network |
| title_full_unstemmed | Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network |
| title_short | Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network |
| title_sort | detecting protein complexes based on a combination of topological and biological properties in protein protein interaction network |
| url | http://www.sciencedirect.com/science/article/pii/S1687157X17301117 |
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