ArticleScientific reports2017
Unified Alignment of Protein-Protein Interaction Networks.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Exact p-values for global network alignments via combinatorial analysis of shared GO terms : REFANGO: Rigorous Evaluation of Functional Alignments of Networks using Gene Ontology.Journal of mathematical biology · 2024Article
- SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment.NPJ systems biology and applications · 2022Article
- Challenges and Limitations of Biological Network Analysis.Biotech (Basel (Switzerland)) · 2022Article
- An Extensive Assessment of Network Embedding in PPI Network Alignment.Entropy (Basel, Switzerland) · 2022Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- BioAlign: An Accurate Global PPI Network Alignment Algorithm.Evolutionary bioinformatics online · 2022Article
- Juxtapose: a gene-embedding approach for comparing co-expression networks.BMC bioinformatics · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- AligNet: alignment of protein-protein interaction networks.BMC bioinformatics · 2020Article
- Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks.BMC bioinformatics · 2020Article
- SAlign-a structure aware method for global PPI network alignment.BMC bioinformatics · 2020Article
- L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks.Scientific reports · 2020Article
- Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma.Biomolecules · 2020Article
- NAIGO: An Improved Method to Align PPI Networks Based on Gene Ontology and Graphlets.Frontiers in bioengineering and biotechnology · 2020Article
- Validation and quality assessment of macromolecular structures using complex network analysis.Scientific reports · 2019Article
- Network Medicine in the Age of Biomedical Big Data.Frontiers in genetics · 2019Review
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Authors and funding
3 authors.
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Abstract
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.
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