NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Woo, Hyun-Myung; Jeong, Hyundoo; Yoon, Byung-Jun

doi:10.1371/journal.pone.0227598

Title: NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Journal Article · 26 January 2020 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0227598 · OSTI ID:1629157

^[1]; Jeong, Hyundoo ^[2]; Yoon, Byung-Jun ^[3]

Texas A & M Univ., College Station, TX (United States). Dept. of Electrical and Computer Engineering; DOE/OSTI
Incheon National Univ. (Korea, Republic of). Dept. of Mechatronics Engineering
Texas A & M Univ., College Station, TX (United States). Dept. of Electrical and Computer Engineering; Texas A & M Univ., College Station, TX (United States). TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering; Brookhaven National Lab. (BNL), Upton, NY (United States). Computational Science Initiative

Comparative network analysis provides effective computational means for gaining novel insights into the structural and functional compositions of biological networks. In recent years, various methods have been developed for biological network alignment, whose main goal is to identify important similarities and critical differences between networks in terms of their topology and composition. A major impediment to advancing network alignment techniques has been the lack of gold-standard benchmarks that can be used for accurate and comprehensive performance assessment of such algorithms. The original NAPAbench (network alignment performance assessment benchmark) was developed to address this problem, and it has been widely utilized by many researchers for the development, evaluation, and comparison of novel network alignment techniques. In this work, we introduce NAPAbench 2—a major update of the original NAPAbench that was introduced in 2012. NAPAbench 2 includes a completely redesigned network synthesis algorithm that can generate protein-protein interaction (PPI) network families whose characteristics closely match those of the latest real PPI networks. Furthermore, the network synthesis algorithm comes with an intuitive GUI that allows users to easily generate PPI network families with an arbitrary number of networks of any size, according to a flexible user-defined phylogeny. In addition, NAPAbench 2 provides updated benchmark datasets—created using the redesigned network synthesis algorithm—which can be used for comprehensive performance assessment of network alignment algorithms and their scalability.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: SC0012704

OSTI ID:: 1629157

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 1 Vol. 15; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (82)

Transglutaminase 2: a multi-functional protein in multiple subcellular compartments Park, Donghyun; Choi, Sun Shim; Ha, Kwon-Soo Amino Acids, Vol. 39, Issue 3 https://doi.org/10.1007/s00726-010-0500-z	journal	February 2010
IPAVS: Integrated Pathway Resources, Analysis, and Visualization System Kumar Sreenivasaiah, Pradeep; Rani, Shilpa; Cayetano, Joseph Biophysical Journal, Vol. 102, Issue 3 https://doi.org/10.1016/j.bpj.2011.11.997	journal	January 2012
SUMONA: A supervised method for optimizing network alignment Tuncay, Erhun Giray; Can, Tolga Computational Biology and Chemistry, Vol. 63 https://doi.org/10.1016/j.compbiolchem.2016.03.003	journal	August 2016
Ribosomal protein S3: A multi-functional protein that interacts with both p53 and MDM2 through its KH domain Yadavilli, Sridevi; Mayo, Lindsey D.; Higgins, Maureen DNA Repair, Vol. 8, Issue 10 https://doi.org/10.1016/j.dnarep.2009.07.003	journal	October 2009
Transient Protein-Protein Interactions: Structural, Functional, and Network Properties Perkins, James R.; Diboun, Ilhem; Dessailly, Benoit H. Structure, Vol. 18, Issue 10 https://doi.org/10.1016/j.str.2010.08.007	journal	October 2010
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Drp1 modulates mitochondrial stress responses to mitotic arrest Peña-Blanco, Aida; Haschka, Manuel D.; Jenner, Andreas Cell Death & Differentiation, Vol. 27, Issue 9 https://doi.org/10.1038/s41418-020-0527-y	journal	March 2020
Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes Vangelisti, Alberto; Guidi, Lucia; Cavallini, Andrea Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58878-8	journal	February 2020
Preterm infants with isolated cerebellar hemorrhage show bilateral cortical alterations at term equivalent age Dijkshoorn, Aicha B. C.; Turk, Elise; Hortensius, Lisa M. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-62078-9	journal	March 2020
Modelling the Yeast Interactome Janjić, Vuk; Sharan, Roded; Pržulj, Nataša Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep04273	journal	March 2014
Protein complexes and functional modules in molecular networks Spirin, V.; Mirny, L. A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 21 https://doi.org/10.1073/pnas.2032324100	journal	September 2003
Joint Alignment of Multiple Protein–Protein Interaction Networks via Convex Optimization Hashemifar, Somaye; Huang, Qixing; Xu, Jinbo Journal of Computational Biology, Vol. 23, Issue 11 https://doi.org/10.1089/cmb.2016.0025	journal	November 2016
Choosing appropriate models for protein–protein interaction networks: a comparison study Shao, Mingyu; Yang, Yi; Guan, Jihong Briefings in Bioinformatics, Vol. 15, Issue 5 https://doi.org/10.1093/bib/bbt014	journal	March 2013
SPINAL: scalable protein interaction network alignment Aladağ, Ahmet E.; Erten, Cesim Bioinformatics, Vol. 29, Issue 7 https://doi.org/10.1093/bioinformatics/btt071	journal	February 2013
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks Alkan, Ferhat; Erten, Cesim Bioinformatics, Vol. 30, Issue 4 https://doi.org/10.1093/bioinformatics/btt713	journal	December 2013
A multiobjective memetic algorithm for PPI network alignment Clark, Connor; Kalita, Jugal Bioinformatics, Vol. 31, Issue 12 https://doi.org/10.1093/bioinformatics/btv063	journal	February 2015
L-GRAAL: Lagrangian graphlet-based network aligner Malod-Dognin, Noël; Pržulj, Nataša Bioinformatics, Vol. 31, Issue 13 https://doi.org/10.1093/bioinformatics/btv130	journal	February 2015
DIP: the Database of Interacting Proteins Xenarios, I. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.289	journal	January 2000
Human protein reference database as a discovery resource for proteomics Peri, S. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh070	journal	January 2004
MINT: the Molecular INTeraction database Chatr-aryamontri, A.; Ceol, A.; Palazzi, L. M. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl950	journal	January 2007
PID: the Pathway Interaction Database Schaefer, Carl F.; Anthony, Kira; Krupa, Shiva Nucleic Acids Research, Vol. 37, Issue suppl_1 https://doi.org/10.1093/nar/gkn653	journal	October 2008
IsoBase: a database of functionally related proteins across PPI networks Park, D.; Singh, R.; Baym, M. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1234	journal	December 2010
The IntAct molecular interaction database in 2012 Kerrien, S.; Aranda, B.; Breuza, L. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1088	journal	November 2011
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Szklarczyk, Damian; Morris, John H.; Cook, Helen Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw937	journal	October 2016
New approach for understanding genome variations in KEGG Kanehisa, Minoru; Sato, Yoko; Furumichi, Miho Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky962	journal	October 2018
Modelling protein–protein interaction networks via a stickiness index Pržulj, Nataša; Higham, Desmond J. Journal of The Royal Society Interface, Vol. 3, Issue 10 https://doi.org/10.1098/rsif.2006.0147	journal	August 2006
Amino acid repeat patterns in protein sequences: Their diversity and structural-functional implications Katti, Mukund V.; Sami-Subbu, R.; Ranjekar, Prabhakar K. Protein Science, Vol. 9, Issue 6 https://doi.org/10.1110/ps.9.6.1203	journal	January 2000
Accurate multiple network alignment through context-sensitive random walk Jeong, Hyundoo; Yoon, Byung-Jun BMC Systems Biology, Vol. 9, Issue Suppl 1 https://doi.org/10.1186/1752-0509-9-s1-s7	journal	January 2015
A Network Synthesis Model for Generating Protein Interaction Network Families Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0041474	journal	August 2012
SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun PLoS ONE, Vol. 8, Issue 7 https://doi.org/10.1371/journal.pone.0067995	journal	July 2013
GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0098750	journal	June 2014
Optimal Network Alignment with Graphlet Degree Vectors Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne Cancer Informatics, Vol. 9 https://doi.org/10.4137/cin.s4744	journal	January 2010
Biological network comparison using graphlet degree distribution Przulj, Natasa arXiv https://doi.org/10.48550/arxiv.0901.4589	text	January 2009
Joint alignment of multiple protein-protein interaction networks via convex optimization Hashemifar, Somaye; Huang, Qixing; Xu, Jinbo arXiv https://doi.org/10.48550/arxiv.1604.03482	preprint	January 2016
Transglutaminase 2: a multi-functional protein in multiple subcellular compartments Park, Donghyun; Choi, Sun Shim; Ha, Kwon-Soo Amino Acids, Vol. 39, Issue 3 https://doi.org/10.1007/s00726-010-0500-z	journal	February 2010
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
IPAVS: Integrated Pathway Resources, Analysis, and Visualization System Kumar Sreenivasaiah, Pradeep; Rani, Shilpa; Cayetano, Joseph Biophysical Journal, Vol. 102, Issue 3 https://doi.org/10.1016/j.bpj.2011.11.997	journal	January 2012
SUMONA: A supervised method for optimizing network alignment Tuncay, Erhun Giray; Can, Tolga Computational Biology and Chemistry, Vol. 63 https://doi.org/10.1016/j.compbiolchem.2016.03.003	journal	August 2016
Ribosomal protein S3: A multi-functional protein that interacts with both p53 and MDM2 through its KH domain Yadavilli, Sridevi; Mayo, Lindsey D.; Higgins, Maureen DNA Repair, Vol. 8, Issue 10 https://doi.org/10.1016/j.dnarep.2009.07.003	journal	October 2009
Transient Protein-Protein Interactions: Structural, Functional, and Network Properties Perkins, James R.; Diboun, Ilhem; Dessailly, Benoit H. Structure, Vol. 18, Issue 10 https://doi.org/10.1016/j.str.2010.08.007	journal	October 2010
PID: The Pathway Interaction Database Schaefer, Carl; Anthony, Kira; Krupa, Shiva Nature Precedings https://doi.org/10.1038/npre.2008.2243.1	journal	August 2008
Topological network alignment uncovers biological function and phylogeny Kuchaiev, Oleksii; Milenkovic, Tijana; Memisevic, Vesna Nature Precedings https://doi.org/10.1038/npre.2009.4089.1	journal	December 2009
Network biology: understanding the cell's functional organization Barabási, Albert-László; Oltvai, Zoltán N. Nature Reviews Genetics, Vol. 5, Issue 2 https://doi.org/10.1038/nrg1272	journal	February 2004
The Transcription Factor-microRNA Regulatory Network during hESC-chondrogenesis Griffiths, Rosie; Woods, Steven; Cheng, Aixin Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-61734-4	journal	March 2020
Modelling the Yeast Interactome Janjić, Vuk; Sharan, Roded; Pržulj, Nataša Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep04273	journal	March 2014
Protein complexes and functional modules in molecular networks Spirin, V.; Mirny, L. A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 21 https://doi.org/10.1073/pnas.2032324100	journal	September 2003
Joint Alignment of Multiple Protein–Protein Interaction Networks via Convex Optimization Hashemifar, Somaye; Huang, Qixing; Xu, Jinbo Journal of Computational Biology, Vol. 23, Issue 11 https://doi.org/10.1089/cmb.2016.0025	journal	November 2016
Choosing appropriate models for protein–protein interaction networks: a comparison study Shao, Mingyu; Yang, Yi; Guan, Jihong Briefings in Bioinformatics, Vol. 15, Issue 5 https://doi.org/10.1093/bib/bbt014	journal	March 2013
Biological network comparison using graphlet degree distribution Przulj, N. Bioinformatics, Vol. 23, Issue 2 https://doi.org/10.1093/bioinformatics/btl301	journal	January 2007
Biological network comparison using graphlet degree distribution Przulj, N. Bioinformatics, Vol. 26, Issue 6 https://doi.org/10.1093/bioinformatics/btq091	journal	March 2010
SPINAL: scalable protein interaction network alignment Aladağ, Ahmet E.; Erten, Cesim Bioinformatics, Vol. 29, Issue 7 https://doi.org/10.1093/bioinformatics/btt071	journal	February 2013
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks Alkan, Ferhat; Erten, Cesim Bioinformatics, Vol. 30, Issue 4 https://doi.org/10.1093/bioinformatics/btt713	journal	December 2013
A multiobjective memetic algorithm for PPI network alignment Clark, Connor; Kalita, Jugal Bioinformatics, Vol. 31, Issue 12 https://doi.org/10.1093/bioinformatics/btv063	journal	February 2015
L-GRAAL: Lagrangian graphlet-based network aligner Malod-Dognin, Noël; Pržulj, Nataša Bioinformatics, Vol. 31, Issue 13 https://doi.org/10.1093/bioinformatics/btv130	journal	February 2015
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
DIP: the Database of Interacting Proteins Xenarios, I. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.289	journal	January 2000
BIND--The Biomolecular Interaction Network Database Bader, G. D. Nucleic Acids Research, Vol. 29, Issue 1 https://doi.org/10.1093/nar/29.1.242	journal	January 2001
BIND: the Biomolecular Interaction Network Database Bader, G. D. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg056	journal	January 2003
Human protein reference database as a discovery resource for proteomics Peri, S. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh070	journal	January 2004
PID: the Pathway Interaction Database Schaefer, Carl F.; Anthony, Kira; Krupa, Shiva Nucleic Acids Research, Vol. 37, Issue suppl_1 https://doi.org/10.1093/nar/gkn653	journal	October 2008
The IntAct molecular interaction database in 2012 Kerrien, S.; Aranda, B.; Breuza, L. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1088	journal	November 2011
IPAVS: Integrated Pathway Resources, Analysis and Visualization System Sreenivasaiah, Pradeep Kumar; Rani, Shilpa; Cayetano, Joseph Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1208	journal	December 2011
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Mi, Huaiyu; Huang, Xiaosong; Muruganujan, Anushya Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1138	journal	November 2016
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Szklarczyk, Damian; Morris, John H.; Cook, Helen Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw937	journal	October 2016
New approach for understanding genome variations in KEGG Kanehisa, Minoru; Sato, Yoko; Furumichi, Miho Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky962	journal	October 2018
Modelling protein–protein interaction networks via a stickiness index Pržulj, Nataša; Higham, Desmond J. Journal of The Royal Society Interface, Vol. 3, Issue 10 https://doi.org/10.1098/rsif.2006.0147	journal	August 2006
Topological network alignment uncovers biological function and phylogeny Kuchaiev, Oleksii; Milenković, Tijana; Memišević, Vesna Journal of The Royal Society Interface, Vol. 7, Issue 50 https://doi.org/10.1098/rsif.2010.0063	journal	March 2010
GREAT: GRaphlet Edge-based network AlignmenT Crawford, Joseph; Milenkovic, Tijana 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) https://doi.org/10.1109/BIBM.2015.7359684	conference	November 2015
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach Yoon, Byung-Jun; Qian, Xiaoning; Sahraeian, Sayed Mohammad Ebrahim IEEE Signal Processing Magazine, Vol. 29, Issue 1 https://doi.org/10.1109/MSP.2011.942819	journal	January 2012
Triangular Alignment (TAME): A Tensor-Based Approach for Higher-Order Network Alignment Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 14, Issue 6 https://doi.org/10.1109/TCBB.2016.2595583	journal	November 2017
Index-Based Network Aligner of Protein-Protein Interaction Networks Elmsallati, Ahed; Msalati, Abdulghani; Kalita, Jugal IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1109/TCBB.2016.2613098	journal	January 2018
Amino acid repeat patterns in protein sequences: Their diversity and structural-functional implications Katti, Mukund V.; Sami-Subbu, R.; Ranjekar, Prabhakar K. Protein Science, Vol. 9, Issue 6 https://doi.org/10.1110/ps.9.6.1203	journal	January 2000
A Model of Large-Scale Proteome Evolution SolÉ, Ricard V.; Pastor-Satorras, Romualdo; Smith, Eric Advances in Complex Systems, Vol. 05, Issue 01 https://doi.org/10.1142/S021952590200047X	journal	March 2002
Modeling of Protein Interaction Networks Vázquez, Alexei; Flammini, Alessandro; Maritan, Amos Complexus, Vol. 1, Issue 1 https://doi.org/10.1159/000067642	journal	December 2002
Accurate multiple network alignment through context-sensitive random walk Jeong, Hyundoo; Yoon, Byung-Jun BMC Systems Biology, Vol. 9, Issue Suppl 1 https://doi.org/10.1186/1752-0509-9-S1-S7	journal	January 2015
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence Kim, Wan Kyu; Marcotte, Edward M. PLoS Computational Biology, Vol. 4, Issue 11 https://doi.org/10.1371/journal.pcbi.1000232	journal	November 2008
A Network Synthesis Model for Generating Protein Interaction Network Families Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0041474	journal	August 2012
SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun PLoS ONE, Vol. 8, Issue 7 https://doi.org/10.1371/journal.pone.0067995	journal	July 2013
GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0098750	journal	June 2014
Optimal Network Alignment with Graphlet Degree Vectors Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne Cancer Informatics, Vol. 9 https://doi.org/10.4137/CIN.S4744	journal	January 2010
Modeling of protein interaction networks Vazquez, A.; Flammini, A.; Maritan, A. arXiv https://doi.org/10.48550/arxiv.cond-mat/0108043	text	January 2001
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Szklarczyk, Damian; Morris, John H.; Cook, Helen Oxford University Press https://doi.org/10.5167/uzh-144858	text	January 2016

Similar Records

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

Journal Article · 2012 · International Journal of Genomics · OSTI ID:1227737

Tian, Wenhong; Samatova, Nagiza F.

MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Journal Article · 2020 · Bioinformatics · OSTI ID:1822355

Woo, Hyun-Myung; Yoon, Byung-Jun

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

Journal Article · 2024 · Journal of Proteome Research · OSTI ID:2483344

Degnan, David J.; Strauch, Clayton W.; Obiri, Moses Y.; +6 more

Related Subjects

42 ENGINEERING
97 MATHEMATICS AND COMPUTING

Title: NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Citation Formats

References (82)

Similar Records

Related Subjects