NatalieQ: a web server for protein-protein interaction network querying

M. El-Kebir, B.W. Brandt, J. Heringa, G.W. Klau

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Background: Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization.Results: Here, we present NatalieQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the Natalie algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NatalieQ with a biological case study involving the Wnt signaling pathway.Conclusions: We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NatalieQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/. © 2014 El-Kebir et al.; licensee BioMed Central Ltd.
Original languageEnglish
Pages (from-to)1-7
Number of pages7
JournalBMC Systems Biology
Volume8
Issue number40
DOIs
Publication statusPublished - 2014

Fingerprint

Protein Interaction Maps
Protein Interaction Networks
Web Server
Protein-protein Interaction
Alignment
Servers
Proteins
Wnt Signaling Pathway
Regulator Genes
Interaction
Signal Transduction
Topology
Signal transduction
Molecular interactions
Signaling Pathways
Biological Networks
Combinatorial optimization
Combinatorial Optimization
Biological systems
Biological Systems

Cite this

El-Kebir, M. ; Brandt, B.W. ; Heringa, J. ; Klau, G.W. / NatalieQ: a web server for protein-protein interaction network querying. In: BMC Systems Biology. 2014 ; Vol. 8, No. 40. pp. 1-7.
@article{705b47af7c9049bab273d38177518704,
title = "NatalieQ: a web server for protein-protein interaction network querying",
abstract = "Background: Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization.Results: Here, we present NatalieQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the Natalie algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NatalieQ with a biological case study involving the Wnt signaling pathway.Conclusions: We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NatalieQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/. {\circledC} 2014 El-Kebir et al.; licensee BioMed Central Ltd.",
author = "M. El-Kebir and B.W. Brandt and J. Heringa and G.W. Klau",
year = "2014",
doi = "10.1186/1752-0509-8-40",
language = "English",
volume = "8",
pages = "1--7",
journal = "BMC Systems Biology",
issn = "1752-0509",
publisher = "BioMed Central",
number = "40",

}

NatalieQ: a web server for protein-protein interaction network querying. / El-Kebir, M.; Brandt, B.W.; Heringa, J.; Klau, G.W.

In: BMC Systems Biology, Vol. 8, No. 40, 2014, p. 1-7.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

T1 - NatalieQ: a web server for protein-protein interaction network querying

AU - El-Kebir, M.

AU - Brandt, B.W.

AU - Heringa, J.

AU - Klau, G.W.

PY - 2014

Y1 - 2014

N2 - Background: Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization.Results: Here, we present NatalieQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the Natalie algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NatalieQ with a biological case study involving the Wnt signaling pathway.Conclusions: We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NatalieQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/. © 2014 El-Kebir et al.; licensee BioMed Central Ltd.

AB - Background: Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization.Results: Here, we present NatalieQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the Natalie algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NatalieQ with a biological case study involving the Wnt signaling pathway.Conclusions: We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NatalieQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/. © 2014 El-Kebir et al.; licensee BioMed Central Ltd.

U2 - 10.1186/1752-0509-8-40

DO - 10.1186/1752-0509-8-40

M3 - Article

VL - 8

SP - 1

EP - 7

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

IS - 40

ER -