The MoVIN server for the analysis of protein interaction networks

Paolo Marcatili, Giovanni Bussotti, Anna Tramontano

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Abstract

Background: Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.Results: Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.Conclusions: The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.
Original languageEnglish
Article numberS11
JournalBMC Bioinformatics
Volume9
Issue numberSuppl. 2
Number of pages8
ISSN1471-2105
DOIs
Publication statusPublished - 2008
Externally publishedYes

Bibliographical note

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords

  • protein interaction
  • Animalia (Animals) - Animalia [33000] animal common
  • 00530, General biology - Information, documentation, retrieval and computer applications
  • 10060, Biochemistry studies - General
  • Computational Biology
  • MoVIN server computer software
  • Biochemistry and Molecular Biophysics
  • Computer Applications

Cite this

Marcatili, Paolo ; Bussotti, Giovanni ; Tramontano, Anna. / The MoVIN server for the analysis of protein interaction networks. In: BMC Bioinformatics. 2008 ; Vol. 9, No. Suppl. 2.
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The MoVIN server for the analysis of protein interaction networks. / Marcatili, Paolo; Bussotti, Giovanni; Tramontano, Anna.

In: BMC Bioinformatics, Vol. 9, No. Suppl. 2, S11, 2008.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - The MoVIN server for the analysis of protein interaction networks

AU - Marcatili, Paolo

AU - Bussotti, Giovanni

AU - Tramontano, Anna

N1 - This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PY - 2008

Y1 - 2008

N2 - Background: Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.Results: Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.Conclusions: The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.

AB - Background: Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.Results: Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.Conclusions: The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.

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KW - Animalia (Animals) - Animalia [33000] animal common

KW - 00530, General biology - Information, documentation, retrieval and computer applications

KW - 10060, Biochemistry studies - General

KW - Computational Biology

KW - MoVIN server computer software

KW - Biochemistry and Molecular Biophysics

KW - Computer Applications

U2 - 10.1186/1471-2105-9-S2-S11

DO - 10.1186/1471-2105-9-S2-S11

M3 - Journal article

VL - 9

JO - B M C Bioinformatics

JF - B M C Bioinformatics

SN - 1471-2105

IS - Suppl. 2

M1 - S11

ER -