L-GRAAL: Lagrangian graphlet-based network aligner

Bioinformatics
Noël Malod-Dognin, Nataša Pržulj

Abstract

Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similar...Continue Reading

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Citations

Jul 1, 2016·Bioinformatics·Lei MengTijana Milenković
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Jun 29, 2018·Bioinformatics·Karel Kalecky, Young-Rae Cho
Nov 14, 2018·Bioinformatics·Thomas GaudeletNataša Pržulj
Mar 2, 2019·Bioinformatics·Noël Malod-Dognin, Nataša Pržulj
Feb 20, 2019·Nature Communications·Noël Malod-DogninNataša Pržulj
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Apr 13, 2018··Huda NassarAnanth Grama

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Methods Mentioned

BETA
two-hybrid
affinity purification
coimmunoprecipitation

Software Mentioned

GHOST
GRAAL
PISWAP
NETAL
MI
BLAST
NATALIE
MAGNA
DUALALIGNER
HOPEMAP

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