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Bioinformatics Advance Access first published online on July 21, 2007
This version published online on July 27, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm373
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

APID2NET: unified interactome graphic analyzer

Juan Hernandez Toro 1, Carlos Prieto 1 and Javier De Las Rivas 1,*

1Bioinformatics and Functional Genomics Research Group, Cancer Research Center (IBMCC-CIC, CSIC-USAL), Salamanca, Spain.

*To whom correspondence should be addressed. Dr. Javier De Las Rivas, E-mail: jrivas{at}usal.es


  Abstract

Motivation: Exploration and analysis of interactome networks at systems level requires unification of the biomolecular elements and annotations that come from many different high-throughput or small-scale proteomic experiments. Only such integration can provide a non-redundant and consistent identification of proteins and interactions. APID2NET is a new tool that works with Cytoscape to allow surfing unified interactome data by querying APID server (http://bioinfow.dep.usal.es/apid/) to provide interactive analysis of protein-protein interaction (PPI) networks. The program is designed to visualize, explore and analyze the proteins and interactions retrieved, including the annotations and attributes associated to them, such as: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs, etc. The tool provides interactive graphical representation of the networks with all Cytoscape capabilities, plus new automatic tools to find concurrent functional and structural attributes along all protein pairs in a network.

Availability: http://bioinfow.dep.usal.es/apid/apid2net.html

Supplementary information: Installation Guide and User’s Guide are supplied at the Web site indicated above.

Contact: jrivas{at}usal.es

Associate Editor: Dr. Trey Ideker

Received on April 13, 2007; revised on June 7, 2007; accepted on July 11, 2007

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