InteroPORC: automated inference of highly conserved protein interaction networks

Motivation: Protein–protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, intero...

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Bibliographic Details
Published in:Bioinformatics 2008-07, Vol.24 (14), p.1625-1631
Main Authors: Michaut, Magali, Kerrien, Samuel, Montecchi-Palazzi, Luisa, Chauvat, Franck, Cassier-Chauvat, Corinne, Aude, Jean-Christophe, Legrain, Pierre, Hermjakob, Henning
Format: Article
Language:English
Subjects:
Algorithms
Automation
Biological and medical sciences
Computational Biology - methods
Computer Simulation
Cyanobacteria - genetics
Cyanobacteria - metabolism
Cyanophyta
Fundamental and applied biological sciences. Psychology
General aspects
Genome, Bacterial
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Biological
Protein Interaction Mapping
Protein Structure, Tertiary
Proteins - chemistry
Signal Processing, Computer-Assisted
Software
Synechocystis
Synechocystis - genetics
Synechocystis - metabolism
Systems Biology
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Summary:Motivation: Protein–protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein interaction networks between organisms. However, no standard tool is available so far for that purpose. Results: In this study, we present an automated prediction tool developed for all sequenced genomes available in Integr8. We also have developed a second method to predict protein–protein interactions in the widely used cyanobacterium Synechocystis. Using these methods, we have constructed a new network of 8783 inferred interactions for Synechocystis. Availability: InteroPORC is open-source, downloadable and usable through a web interface at http://biodev.extra.cea.fr/interoporc/ Contact: michaut.bioinfo@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn249