Domain-oriented edge-based alignment of protein interaction networks.

dc.contributor.author

Guo, Xin

dc.contributor.author

Hartemink, Alexander J

dc.coverage.spatial

England

dc.date.accessioned

2017-08-01T20:49:53Z

dc.date.available

2017-08-01T20:49:53Z

dc.date.issued

2009-06-15

dc.description.abstract

MOTIVATION: Recent advances in high-throughput experimental techniques have yielded a large amount of data on protein-protein interactions (PPIs). Since these interactions can be organized into networks, and since separate PPI networks can be constructed for different species, a natural research direction is the comparative analysis of such networks across species in order to detect conserved functional modules. This is the task of network alignment. RESULTS: Most conventional network alignment algorithms adopt a node-then-edge-alignment paradigm: they first identify homologous proteins across networks and then consider interactions among them to construct network alignments. In this study, we propose an alternative direct-edge-alignment paradigm. Specifically, instead of explicit identification of homologous proteins, we directly infer plausibly alignable PPIs across species by comparing conservation of their constituent domain interactions. We apply our approach to detect conserved protein complexes in yeast-fly and yeast-worm PPI networks, and show that our approach outperforms two recent approaches in most alignment performance metrics. AVAILABILITY: Supplementary material and source code can be found at http://www.cs.duke.edu/ approximately amink/.

dc.identifier

https://www.ncbi.nlm.nih.gov/pubmed/19477994

dc.identifier

btp202

dc.identifier.eissn

1367-4811

dc.identifier.uri

https://hdl.handle.net/10161/15156

dc.language

eng

dc.publisher

Oxford University Press (OUP)

dc.relation.ispartof

Bioinformatics

dc.relation.isversionof

10.1093/bioinformatics/btp202

dc.subject

Algorithms

dc.subject

Computational Biology

dc.subject

Protein Interaction Domains and Motifs

dc.subject

Protein Interaction Mapping

dc.subject

Proteins

dc.subject

Sequence Alignment

dc.title

Domain-oriented edge-based alignment of protein interaction networks.

dc.type

Journal article

duke.contributor.orcid

Hartemink, Alexander J|0000-0002-1292-2606

pubs.author-url

https://www.ncbi.nlm.nih.gov/pubmed/19477994

pubs.begin-page

i240

pubs.end-page

i246

pubs.issue

12

pubs.organisational-group

Computer Science

pubs.organisational-group

Duke

pubs.organisational-group

Trinity College of Arts & Sciences

pubs.publication-status

Published

pubs.volume

25

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