{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:44:42Z","timestamp":1706813082141},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2082,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein\u2013protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism.<\/jats:p>\n               <jats:p>Availability: OrthoNets is freely available at http:\/\/wodaklab.org\/orthonets\/.<\/jats:p>\n               <jats:p>Contact: \u00a0jim.vlasblom@utoronto.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr035","type":"journal-article","created":{"date-parts":[[2011,1,22]],"date-time":"2011-01-22T01:24:02Z","timestamp":1295659442000},"page":"883-884","source":"Crossref","is-referenced-by-count":4,"title":["OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms"],"prefix":"10.1093","volume":"27","author":[{"given":"Yanqi","family":"Hao","sequence":"first","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Merkoulovitch","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Vlasblom","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"},{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuye","family":"Pu","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei L.","family":"Turinsky","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denitza","family":"Roudeva","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"},{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian","family":"Turner","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack","family":"Greenblatt","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"},{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shoshana J.","family":"Wodak","sequence":"additional","affiliation":[{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"},{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"},{"name":"1 Molecular Structure & Function program, Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8, 2Department of Biochemistry, 3Department of Molecular Genetics and 4Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 1 King's College Circle, Toronto ON, Canada M5S 1A8"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,1,20]]},"reference":[{"key":"2023012511551786200_B1","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012511551786200_B2","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1126\/science.1180823","article-title":"The genetic landscape of a cell","volume":"327","author":"Costanzo","year":"2010","journal-title":"Science"},{"key":"2023012511551786200_B3","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nature04532","article-title":"Proteome survey reveals modularity of the yeast cell machinery","volume":"440","author":"Gavin","year":"2006","journal-title":"Nature"},{"key":"2023012511551786200_B4","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2007.02.005","article-title":"Chromatin modifications and their function","volume":"128","author":"Kouzarides","year":"2007","journal-title":"Cell"},{"key":"2023012511551786200_B5","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature04670","article-title":"Global landscape of protein complexes in the yeast Saccharomyces cerevisiae","volume":"440","author":"Krogan","year":"2006","journal-title":"Nature"},{"key":"2023012511551786200_B6","first-page":"811","article-title":"A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency","volume":"9","author":"Mak","year":"2010","journal-title":"MCP"},{"key":"2023012511551786200_B7","volume-title":"Online Mendelian Inheritance in Man, OMIM.","author":"McKusick","year":"2006"},{"key":"2023012511551786200_B8","doi-asserted-by":"crossref","first-page":"D476","DOI":"10.1093\/nar\/gki107","article-title":"Inparanoid: a comprehensive database of eukaryotic orthologs","volume":"33","author":"O'Brien","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012511551786200_B9","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/1471-2105-9-405","article-title":"iRefIndex: a consolidated protein interaction database with provenance","volume":"9","author":"Razick","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012511551786200_B10","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012511551786200_B11","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein-protein interaction network: a resource for annotating the proteome","volume":"122","author":"Stelzl","year":"2005","journal-title":"Cell"},{"key":"2023012511551786200_B12","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baq023","article-title":"iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence","volume":"2010","author":"Turner","year":"2010","journal-title":"Database"},{"key":"2023012511551786200_B13","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs","volume":"14","author":"Yu","year":"2004","journal-title":"Genome Res."},{"key":"2023012511551786200_B14","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1101\/gad.1292105","article-title":"The human PAF complex coordinates transcription with events downstream of RNA synthesis","volume":"19","author":"Zhu","year":"2005","journal-title":"Genes Dev."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/6\/883\/48865825\/bioinformatics_27_6_883.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/6\/883\/48865825\/bioinformatics_27_6_883.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:08:57Z","timestamp":1674648537000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/6\/883\/236896"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,20]]},"references-count":14,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2011,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr035","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,3,15]]},"published":{"date-parts":[[2011,1,20]]}}}