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An Iteration Method for Identifying Yeast Essential Proteins from Weighted PPI Network based on topological and functional features of proteins

Shiyuan Li, Zhiping Chen, Xin He, Zhen Zhang, Tingrui Pei, Yihong Tan, Lei Wang
2020 IEEE Access  
.: Iteration Method for Identifying Yeast Essential Proteins From Weighted PPI Network efficient prediction methods to identify potential essential proteins [1]-[3].  ...  And then, based on weighted PPI networks and information of orthologous proteins, some critical network topological features and protein functional features will be extracted for each protein in the weighted  ...  ACKNOWLEDGMENT (Shiyuan Li and Zhiping Chen are co-first authors.)  ... 
doi:10.1109/access.2020.2993860 fatcat:rqrwkshpb5aq3ivxcia433gskq

An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity

Xianyou Zhu, Yaocan Zhu, Yihong Tan, Zhiping Chen, Lei Wang
2022 Frontiers in Aging Neuroscience  
After that, subcellular localization and homologous information of proteins will be integrated to extract functional features for proteins, and based on both functional and topological features obtained  ...  In LNSPF, an original protein-protein interaction (PPI) network will be constructed first based on known protein-protein interaction data downloaded from benchmark databases, based on which, topological  ...  An iteration method for identifying yeast essential proteins from weighted PPI network based on topological and functional features of proteins.  ... 
doi:10.3389/fnagi.2021.799500 pmid:35140599 pmcid:PMC8819145 fatcat:jir6btn7sjc4llylthhcc5c4h4

An iteration method for identifying yeast essential proteins from heterogeneous network

Bihai Zhao, Yulin Zhao, Xiaoxia Zhang, Zhihong Zhang, Fan Zhang, Lei Wang
2019 BMC Bioinformatics  
In RWHN, the topology, conservative and functional features of essential proteins are all taken into account in the prediction process.  ...  Many network topology-based computational methods have been designed to detect essential proteins. However, these methods are limited by the completeness of available PPI data.  ...  Authors' contributions BHZ, ZHZ and LW obtained the protein-protein interaction data, domain data, information on orthologous proteins and the localization information of proteins.  ... 
doi:10.1186/s12859-019-2930-2 fatcat:g34sursdsfb25lne45c5jis7de

Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks

B. Chen, W. Fan, J. Liu, F.-X. Wu
2013 Briefings in Bioinformatics  
of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks.  ...  In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein ^protein interaction (PPI) networks.  ...  [78] propose an iterative scoring method to reassign weights for edges and develop the CMC (Clustering based on Maximal Cliques) method to identify protein complexes from PPI networks.  ... 
doi:10.1093/bib/bbt039 pmid:23780996 fatcat:rqgsiknpgvabrcxjvcz5qqvldy

Identification of Essential Proteins Based on Improved HITS Algorithm

Xiujuan Lei, Siguo Wang, Fang-Xiang Wu
2019 Genes  
In this paper, we propose a novel method by applying Hyperlink-Induced Topic Search (HITS) on weighted PPI networks to detect essential proteins, named HSEP.  ...  Then, both biological information and network topological characteristics are taken into account to weighted PPI networks.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes10020177 pmid:30823614 pmcid:PMC6409685 fatcat:abjkeozzpjbvxdmzorbc7kbp3a

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks

Wei Peng, Jianxin Wang, Weiping Wang, Qing Liu, Fang-Xiang Wu, Yi Pan
2012 BMC Systems Biology  
Many computational methods have been proposed for predicting essential proteins by using the topological features of protein-protein interaction (PPI) networks.  ...  Differently from other methods, ION identifies essential proteins depending on not only the connections between proteins but also their orthologous properties and features of their neighbors.  ...  Acknowledgements We thank our colleagues Min Yang for helpful discussion about program convergence and Min Li  ... 
doi:10.1186/1752-0509-6-87 pmid:22808943 pmcid:PMC3472210 fatcat:l6mgjpbbubbihcry462oalwymi

Identification and prediction of functional protein modules using a bi-level community detection algorithm

Suely Oliveira, Rahil Sharma
2016 International Journal of Bioinformatics Research and Applications  
Based on these communities found, we make predictions of functional modules for 57 uncharacterised proteins in our dataset, with 80%+ accuracy.  ...  Using this algorithm, we extract 123 communities from a protein-protein interaction (PPI) network involving 2361 proteins and 7182 interactions in Saccharomyces cerevisiae i.e. yeast.  ...  Acknowledgement We would like to thank the reviewers for their time and helpful advice.  ... 
doi:10.1504/ijbra.2016.077124 fatcat:5zmf4viidjdgvirtbontvvl6s4

Essential Protein Identification From Protein Networks Using Topological And Biological Properties

FathimaShabnam CB, Sminu Izudheen.
2016 International Journal of Advanced Research  
Based on this fact the algorithm UDoNC predicted the essential proteins from the PPI data. An example of a protein that contains multiple SH3 domains is the cytoplasmic protein Nck.  ...  It is said that essential proteins are more conserved than non-essential protein and using that concept (Peng et al,2012) developed an iteration method named ION considering the orthology with PPI network  ...  As the application areas are disease diagnosis, drug analysis and cosmetics, we could predict the importance of essential gene in these areas.  ... 
doi:10.21474/ijar01/1179 fatcat:kzgyd4gvyvg5rhtwq5n2riedfe

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes

Sriganesh Srihari, Chern Han Yong, Ashwini Patil, Limsoon Wong
2015 FEBS Letters  
In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI  ...  We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight challenges faced by these methods, in particular detection of sparse and small or sub- complexes and discerning  ...  Alison Anderson (The University of Queensland) for critical reading of the manuscript. S.S. is supported by an Australian National Health and Medical Research Council (NHMRC) Grant# 1028742.  ... 
doi:10.1016/j.febslet.2015.04.026 pmid:25913176 fatcat:kumgbvumnbdenapibxn4kaf5wa

Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network

Bo Xu, Yu Liu, Chi Lin, Jie Dong, Xiaoxia Liu, Zengyou He
2018 Frontiers in Genetics  
Identifying protein complexes from protein-protein interaction networks (PPINs) is important to understand the science of cellular organization and function.  ...  According to the score of protein pairs, we considered the top ranked ones as reliable PPI and the score as the weight of edge between two distinct proteins.  ...  FUNDING This work is supported by the grants from the Natural Science Foundation of China (No. 61502071 and 61572094) and the Fundamental Research Funds for the Central Universities (No.DUT16RC(4)63).  ... 
doi:10.3389/fgene.2018.00272 pmid:30087694 pmcid:PMC6067004 fatcat:67rzow3zgjejdequhgg5s77knq

Assessing and predicting protein interactions by combining manifold embedding with multiple information integration

Ying-Ke Lei, Zhu-Hong You, Zhen Ji, Lin Zhu, De-Shuang Huang
2012 BMC Bioinformatics  
Validation of the proposed method was performed with extensive experiments on densely-connected and sparse PPI networks of yeast respectively.  ...  Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism.  ...  [8] introduced an index called FSWeight that exploits indirect neighbors to predict protein functions. These network-topology-based methods do yield impressive results on some benchmark data sets.  ... 
doi:10.1186/1471-2105-13-s7-s3 pmid:22595000 pmcid:PMC3348017 fatcat:qmg2sykaizeepanqtj27vjp6tu

An Ensemble Learning Framework for Detecting Protein Complexes From PPI Networks

Rongquan Wang, Huimin Ma, Caixia Wang
2022 Frontiers in Genetics  
The ELF-DPC first constructs the weighted PPI network by combining topological and biological information.  ...  Therefore, we propose an Ensemble Learning Framework for Detecting Protein Complexes (ELF-DPC) within protein-protein interaction (PPI) networks to address these challenges.  ...  ., 2009) used an iterative method to weight PPI networks and developed a maximal clique-based method (CMC) to discover protein complexes from weighted PPI networks. Wang et al.  ... 
doi:10.3389/fgene.2022.839949 pmid:35281831 pmcid:PMC8908451 fatcat:vi7auscobjbdhbw7iof3xepqee

A supervised protein complex prediction method with network representation learning and gene ontology knowledge

Xiaoxu Wang, Yijia Zhang, Peixuan Zhou, Xiaoxia Liu
2022 BMC Bioinformatics  
This method first constructs a weighted PPI network based on gene ontology knowledge and topology information, reducing the network's noise problem.  ...  Background Protein complexes are essential for biologists to understand cell organization and function effectively.  ...  Acknowledgements All authors would like to thank the reviewers for the valuable comments. Author contributions YZ, XL, and XW designed the method and experiments.  ... 
doi:10.1186/s12859-022-04850-4 pmid:35879648 pmcid:PMC9317086 fatcat:f7ne3xtxbzfardnbefagpmuhuq

Computational prediction and analysis of protein-protein interaction networks [article]

Somaye Hashemifar
2017 arXiv   pre-print
The talk will consist of two parts. I will discuss several methods for protein-protein interaction network alignment and investigate their preferences to other existing methods.  ...  They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional modules and pathways.  ...  and essentiality-based features.  ... 
arXiv:1709.01923v2 fatcat:cy63jpklarbmxbrcvfgzx2ob2q

Identifying essential proteins based on protein domains in protein-protein interaction networks

Jianxin Wang, Wei Peng, Yingjiao Chen, Yu Lu, Yi Pan
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
In this work, we firstly analyze the correlation between the essentiality of proteins and their domain features based on data of 13 species.  ...  However, these methods are limited to the complementation of available protein-protein interaction (PPI) data and depend on the network accuracy.  ...  [19] have proposed an iteration method for predicting essential proteins by integrating the orthology with PPI networks.  ... 
doi:10.1109/bibm.2013.6732476 dblp:conf/bibm/WangPCLP13 fatcat:j5rhwjigebc37dyecb37lksuwm
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