title: The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis.
abstract: BACKGROUND
  This work was motivated by the need for an automated tool for discovery of genetic networks and the availability of extensive contextual protein-protein interaction information in the iHOP repository. At the moment, this information cannot be explored to its full potential due to the lack of software tools to reliably collect, process and display that information in a way that life scientists can quickly analyze genes of interest and search for potential interaction networks. Commercial tools can perform a similar job, but results appear to be less informative than those obtained using contextual information.
  
  
  RESULTS
  The Gene Interaction Miner (GIM) could successfully uncover complex network structures of protein-protein interactions for a test dataset composed of genes already related to Alzheimer's disease. That same set, when examined using two other analysis tools, namely STRING and Pathway Studio, resulted in incomplete protein-protein interaction networks, which indicate that the use of curated databases only gives a partial picture of the biological processes behind the disease.
  
  
  BACKGROUND
  The dataset used in this work and a running version of the software tool is available for download from the web site http://www.cs.newcastle.edu.au/~mendes/softwareGIM.html.
authors: School of Electrical Engineering and Computer Science The University of Newcastle, Callaghan, NSW, 2308, Australia.
authors: Aaron
authors: A
authors: Ikin
authors: Carlos
authors: C
authors: Riveros
authors: Pablo
authors: P
authors: Moscato
authors: Alexandre
authors: A
authors: Mendes
mesh_terms: D001665:Binding Sites; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins