Predicting overlapping protein complexes based on core-attachment and a local modularity structure
Abstract Background In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that work very well for identifying PCs. However, most of existing methods us...
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doaj-d4ffdddb95044b99899a3e96cb6066312020-11-25T00:04:24ZengBMCBMC Bioinformatics1471-21052018-08-0119111510.1186/s12859-018-2309-9Predicting overlapping protein complexes based on core-attachment and a local modularity structureRongquan Wang0Guixia Liu1Caixia Wang2Lingtao Su3Liyan Sun4College of Computer Science and Technology, Jilin UniversityCollege of Computer Science and Technology, Jilin UniversitySchool of International Economics, China Foreign Affairs UniversityCollege of Computer Science and Technology, Jilin UniversityCollege of Computer Science and Technology, Jilin UniversityAbstract Background In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that work very well for identifying PCs. However, most of existing methods usually overlook the inherent core-attachment organization of PCs. Therefore, these methods have three major limitations we should concern. Firstly, many methods have ignored the importance of selecting seed, especially without considering the impact of overlapping nodes as seed nodes. Thus, there may be false predictions. Secondly, PCs are generally supposed to be dense subgraphs. However, the subgraphs with high local modularity structure usually correspond to PCs. Thirdly, a number of available methods lack handling noise mechanism, and miss some peripheral proteins. In summary, all these challenging issues are very important for predicting more biological overlapping PCs. Results In this paper, to overcome these weaknesses, we propose a clustering method by core-attachment and local modularity structure, named CALM, to detect overlapping PCs from weighted PPINs with noises. Firstly, we identify overlapping nodes and seed nodes. Secondly, for a node, we calculate the support function between a node and a cluster. In CALM, a cluster which initially consists of only a seed node, is extended by adding its direct neighboring nodes recursively according to the support function, until this cluster forms a locally optimal modularity subgraph. Thirdly, we repeat this process for the remaining seed nodes. Finally, merging and removing procedures are carried out to obtain final predicted clusters. The experimental results show that CALM outperforms other classical methods, and achieves ideal overall performance. Furthermore, CALM can match more complexes with a higher accuracy and provide a better one-to-one mapping with reference complexes in all test datasets. Additionally, CALM is robust against the high rate of noise PPIN. Conclusions By considering core-attachment and local modularity structure, CALM could detect PCs much more effectively than some representative methods. In short, CALM could potentially identify previous undiscovered overlapping PCs with various density and high modularity.http://link.springer.com/article/10.1186/s12859-018-2309-9Protein-protein interaction networksProtein complexOverlapping nodeSeed-extension paradigmCore-attachment and local modularity structureNode betweenness |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rongquan Wang Guixia Liu Caixia Wang Lingtao Su Liyan Sun |
spellingShingle |
Rongquan Wang Guixia Liu Caixia Wang Lingtao Su Liyan Sun Predicting overlapping protein complexes based on core-attachment and a local modularity structure BMC Bioinformatics Protein-protein interaction networks Protein complex Overlapping node Seed-extension paradigm Core-attachment and local modularity structure Node betweenness |
author_facet |
Rongquan Wang Guixia Liu Caixia Wang Lingtao Su Liyan Sun |
author_sort |
Rongquan Wang |
title |
Predicting overlapping protein complexes based on core-attachment and a local modularity structure |
title_short |
Predicting overlapping protein complexes based on core-attachment and a local modularity structure |
title_full |
Predicting overlapping protein complexes based on core-attachment and a local modularity structure |
title_fullStr |
Predicting overlapping protein complexes based on core-attachment and a local modularity structure |
title_full_unstemmed |
Predicting overlapping protein complexes based on core-attachment and a local modularity structure |
title_sort |
predicting overlapping protein complexes based on core-attachment and a local modularity structure |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2018-08-01 |
description |
Abstract Background In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that work very well for identifying PCs. However, most of existing methods usually overlook the inherent core-attachment organization of PCs. Therefore, these methods have three major limitations we should concern. Firstly, many methods have ignored the importance of selecting seed, especially without considering the impact of overlapping nodes as seed nodes. Thus, there may be false predictions. Secondly, PCs are generally supposed to be dense subgraphs. However, the subgraphs with high local modularity structure usually correspond to PCs. Thirdly, a number of available methods lack handling noise mechanism, and miss some peripheral proteins. In summary, all these challenging issues are very important for predicting more biological overlapping PCs. Results In this paper, to overcome these weaknesses, we propose a clustering method by core-attachment and local modularity structure, named CALM, to detect overlapping PCs from weighted PPINs with noises. Firstly, we identify overlapping nodes and seed nodes. Secondly, for a node, we calculate the support function between a node and a cluster. In CALM, a cluster which initially consists of only a seed node, is extended by adding its direct neighboring nodes recursively according to the support function, until this cluster forms a locally optimal modularity subgraph. Thirdly, we repeat this process for the remaining seed nodes. Finally, merging and removing procedures are carried out to obtain final predicted clusters. The experimental results show that CALM outperforms other classical methods, and achieves ideal overall performance. Furthermore, CALM can match more complexes with a higher accuracy and provide a better one-to-one mapping with reference complexes in all test datasets. Additionally, CALM is robust against the high rate of noise PPIN. Conclusions By considering core-attachment and local modularity structure, CALM could detect PCs much more effectively than some representative methods. In short, CALM could potentially identify previous undiscovered overlapping PCs with various density and high modularity. |
topic |
Protein-protein interaction networks Protein complex Overlapping node Seed-extension paradigm Core-attachment and local modularity structure Node betweenness |
url |
http://link.springer.com/article/10.1186/s12859-018-2309-9 |
work_keys_str_mv |
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