{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,22]],"date-time":"2025-03-22T09:16:56Z","timestamp":1742635016305},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: This work was motivated by the need for an automated tool for discovery of genetic networks and the availability of extensive contextual protein\u2013protein 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.<\/jats:p>\n               <jats:p>Results: The Gene Interaction Miner (GIM) could successfully uncover complex network structures of protein\u2013protein 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\u2013protein interaction networks, which indicate that the use of curated databases only gives a partial picture of the biological processes behind the disease.<\/jats:p>\n               <jats:p>Availability: 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\/\u223cmendes\/softwareGIM.html.<\/jats:p>\n               <jats:p>Contact: \u00a0alexandre.mendes@newcastle.edu.au<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp652","type":"journal-article","created":{"date-parts":[[2009,12,5]],"date-time":"2009-12-05T02:17:54Z","timestamp":1259979474000},"page":"283-284","source":"Crossref","is-referenced-by-count":5,"title":["The Gene Interaction Miner: a new tool for data mining contextual information for protein\u2013protein interaction analysis"],"prefix":"10.1093","volume":"26","author":[{"given":"Aaron","family":"Ikin","sequence":"first","affiliation":[{"name":"1 School of Electrical Engineering and Computer Science and 2 Research Centre in Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM), School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, 2308, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Riveros","sequence":"additional","affiliation":[{"name":"1 School of Electrical Engineering and Computer Science and 2 Research Centre in Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM), School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, 2308, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Moscato","sequence":"additional","affiliation":[{"name":"1 School of Electrical Engineering and Computer Science and 2 Research Centre in Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM), School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, 2308, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre","family":"Mendes","sequence":"additional","affiliation":[{"name":"1 School of Electrical Engineering and Computer Science and 2 Research Centre in Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM), School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, 2308, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,12,4]]},"reference":[{"key":"2023012508213127800_B1","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1101\/gr.204102","article-title":"High-throughput imaging of brain gene expression","volume":"12","author":"Brown","year":"2002","journal-title":"Genome Res."},{"key":"2023012508213127800_B2","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/ng0704-664","article-title":"A gene network for navigating the literature","volume":"36","author":"Hoffmann","year":"2004","journal-title":"Nat. Genet."},{"key":"2023012508213127800_B3","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms","volume":"37","author":"Jensen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508213127800_B4","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1093\/bioinformatics\/btg290","article-title":"Pathway studio \u2013 the analysis and navigation of molecular networks","volume":"19","author":"Nikitin","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012508213127800_B5","doi-asserted-by":"crossref","first-page":"2651","DOI":"10.1093\/bioinformatics\/btm401","article-title":"Tools for visually exploring biological networks","volume":"23","author":"Suderman","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/2\/283\/48857059\/bioinformatics_26_2_283.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/2\/283\/48857059\/bioinformatics_26_2_283.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:22:00Z","timestamp":1674634920000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/2\/283\/210285"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,4]]},"references-count":5,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2010,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp652","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,1,15]]},"published":{"date-parts":[[2009,12,4]]}}}