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Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

Nature Precedings

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Title Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
 
Date 2007-06-07T15:27:51Z
 
Creator Jeremy I. Posner
Seth Berger
Avi M. Ma'ayan
 
Subject Biotechnology
Molecular Cell Biology
Bioinformatics
 
Description In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.  Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from 1c;seed 1d; lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.  Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function.
 
Identifier http://precedings.nature.com/documents/35/version/2
oai:nature.com:10101/npre.2007.35.2
http://hdl.handle.net/10101/npre.2007.35.2
 
Source Nature Precedings
 
Type Manuscript
 
Rights Creative Commons Attribution 3.0 License