{"id":"https://openalex.org/W2122815743","doi":"https://doi.org/10.1093/bioinformatics/btn625","title":"Gene expression trends and protein features effectively complement each other in gene function prediction","display_name":"Gene expression trends and protein features effectively complement each other in gene function prediction","publication_year":2008,"publication_date":"2008-12-02","ids":{"openalex":"https://openalex.org/W2122815743","doi":"https://doi.org/10.1093/bioinformatics/btn625","mag":"2122815743","pmid":"https://pubmed.ncbi.nlm.nih.gov/19050035"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn625","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn625","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024587194","display_name":"Krzysztof Wabnik","orcid":"https://orcid.org/0000-0001-7263-0560"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":true,"raw_author_name":"Krzysztof Wabnik","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022568938","display_name":"Torgeir R. Hvidsten","orcid":"https://orcid.org/0000-0001-6097-2539"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Torgeir R. Hvidsten","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019773604","display_name":"Anna Kedzierska","orcid":null},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Anna Kedzierska","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046816327","display_name":"Jelle Van Leene","orcid":"https://orcid.org/0000-0002-4932-8192"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Jelle Van Leene","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004210367","display_name":"Geert De Jaeger","orcid":"https://orcid.org/0000-0001-6558-5669"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Geert De Jaeger","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073611563","display_name":"Gerrit T.S. Beemster","orcid":"https://orcid.org/0000-0001-6014-053X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Gerrit T. S. Beemster","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":false,"raw_author_name":"Jan Komorowski","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077915624","display_name":"Martin Kuiper","orcid":"https://orcid.org/0000-0002-1171-9876"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210120671","display_name":"Ume\u00e5 Plant Science Centre","ror":"https://ror.org/02ehp0f77","country_code":"SE","type":"facility","lineage":["https://openalex.org/I298625061","https://openalex.org/I4210120671","https://openalex.org/I90267481"]},{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["BE","ES","SE"],"is_corresponding":true,"raw_author_name":"Martin T. R. Kuiper","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB Technologiepark 927, 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium, 3The Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, SE-751 24 Uppsala, 4Ume\u00e5 Plant Science Centre, Department of Plant Physiology, Ume\u00e5 University, SE-901 87 Ume\u00e5, Sweden, 5Bioinformatics and Genomics Group, Center for Genomic Regulation (CRG) and Department of Applied Mathematics I, Polytechnic University of Catalonia, Barcelona, Spain and 6Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway","institution_ids":["https://openalex.org/I4210120671","https://openalex.org/I123387679","https://openalex.org/I9617848","https://openalex.org/I32597200","https://openalex.org/I90267481"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5024587194","https://openalex.org/A5077915624"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I32597200","https://openalex.org/I4210120671","https://openalex.org/I90267481","https://openalex.org/I9617848"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2778,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.61156915,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"25","issue":"3","first_page":"322","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7896999716758728,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7896999716758728,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.11259999871253967,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11063","display_name":"Rough Sets and Fuzzy Logic","score":0.04170000180602074,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.6641717553138733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5838611125946045},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5437586903572083},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5415977835655212},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.49650293588638306},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4694463908672333},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4623023569583893},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37837833166122437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36996883153915405},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2785566449165344},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15761122107505798}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.6641717553138733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5838611125946045},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5437586903572083},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5415977835655212},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.49650293588638306},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4694463908672333},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4623023569583893},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37837833166122437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36996883153915405},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2785566449165344},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15761122107505798}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn625","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn625","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19050035","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19050035","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:archive.ugent.be:528653","is_oa":false,"landing_page_url":"https://biblio.ugent.be/publication/528653","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.699999988079071,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1508312564","https://openalex.org/W1529875323","https://openalex.org/W1548332411","https://openalex.org/W1556472699","https://openalex.org/W1557923305","https://openalex.org/W1566527164","https://openalex.org/W1586066135","https://openalex.org/W1589421922","https://openalex.org/W1605637875","https://openalex.org/W1680392829","https://openalex.org/W1970156673","https://openalex.org/W1976526581","https://openalex.org/W1976770091","https://openalex.org/W1987144436","https://openalex.org/W1987678450","https://openalex.org/W1998261914","https://openalex.org/W2017698196","https://openalex.org/W2051027871","https://openalex.org/W2058879468","https://openalex.org/W2059853480","https://openalex.org/W2083870231","https://openalex.org/W2085674480","https://openalex.org/W2090766471","https://openalex.org/W2096280725","https://openalex.org/W2100744200","https://openalex.org/W2102794349","https://openalex.org/W2103017472","https://openalex.org/W2123157758","https://openalex.org/W2125010848","https://openalex.org/W2125973383","https://openalex.org/W2128936012","https://openalex.org/W2129324484","https://openalex.org/W2130925474","https://openalex.org/W2134788911","https://openalex.org/W2135470984","https://openalex.org/W2144810924","https://openalex.org/W2149729839","https://openalex.org/W2150760649","https://openalex.org/W2152689720","https://openalex.org/W2153571621","https://openalex.org/W2160326647","https://openalex.org/W2164628006","https://openalex.org/W2166360158","https://openalex.org/W2167155713","https://openalex.org/W2171030481","https://openalex.org/W2174160981","https://openalex.org/W2298168480","https://openalex.org/W2595408825","https://openalex.org/W2917431650","https://openalex.org/W6633510849","https://openalex.org/W6637386731","https://openalex.org/W6644243236","https://openalex.org/W6649604308","https://openalex.org/W6675346500","https://openalex.org/W6679148343","https://openalex.org/W6683359153"],"related_works":["https://openalex.org/W4292634579","https://openalex.org/W2964314049","https://openalex.org/W2022326234","https://openalex.org/W1531941329","https://openalex.org/W4388694323","https://openalex.org/W3215098729","https://openalex.org/W4243081378","https://openalex.org/W1979330259","https://openalex.org/W2622356054","https://openalex.org/W2109175855"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genome-scale":[1],"'omics'":[2],"data":[3,38,111,181,280],"constitute":[4],"a":[5,19,41,50,94,109,210],"potentially":[6],"rich":[7],"source":[8],"of":[9,21,35,85,97,105,147,163,179,208],"information":[10,73,91],"about":[11],"biological":[12],"systems":[13],"and":[14,23,33,120,130,153,168,238,247,281],"their":[15],"function.":[16],"There":[17],"is":[18,40,49,289],"plethora":[20],"tools":[22],"methods":[24,55],"available":[25,298],"to":[26,56,70,81,88,127,143,165,195,201,268],"mine":[27],"omics":[28,37],"data.":[29,63],"However,":[30],"the":[31,83,103,145,243,253,292],"diversity":[32],"complexity":[34],"different":[36],"types":[39],"stumbling":[42],"block":[43],"for":[44,53,108,171,204,252],"multi-data":[45],"integration,":[46],"hence":[47],"there":[48],"dire":[51],"need":[52],"additional":[54],"exploit":[57],"potential":[58],"synergy":[59,275],"from":[60,193,232,276],"integrated":[61],"orthogonal":[62],"Rough":[64,86,106,286],"Sets":[65,87,107],"provide":[66],"an":[67],"efficient":[68],"means":[69],"use":[71,104],"complex":[72],"in":[74,93,150,239,242,291],"classification":[75,96],"approaches.":[76],"Here,":[77],"we":[78,225],"set":[79],"out":[80],"explore":[82],"possibilities":[84],"incorporate":[89],"diverse":[90],"sources":[92],"functional":[95],"unknown":[98,148,206],"genes.":[99],"RESULTS:":[100],"We":[101],"explored":[102],"novel":[110],"integration":[112],"strategy":[113],"where":[114],"gene":[115,186,278],"expression":[116,187,279],"data,":[117],"protein":[118,282],"features":[119,184],"Gene":[121],"Ontology":[122],"(GO)":[123],"annotations":[124],"were":[125,141,199,213],"combined":[126],"describe":[128],"general":[129],"biologically":[131],"relevant":[132],"patterns":[133],"represented":[134],"by":[135,216,256],"If-Then":[136,157],"rules.":[137],"The":[138,156,259,285],"descriptive":[139],"rules":[140],"used":[142,267],"predict":[144],"function":[146],"genes":[149],"Arabidopsis":[151],"thaliana":[152],"Schizosaccharomyces":[154],"pombe.":[155],"rule":[158],"models":[159,176,198,272],"showed":[160],"success":[161,190],"rates":[162,191],"up":[164],"0.89":[166],"(discriminative":[167],"predictive":[169],"power":[170],"both":[172,233],"modeled":[173],"organisms);":[174],"whereas,":[175],"built":[177],"solely":[178],"one":[180],"type":[182],"(protein":[183],"or":[185,220],"data)":[188],"yielded":[189],"varying":[192],"0.68":[194],"0.78.":[196],"Our":[197],"applied":[200],"generate":[202],"classifications":[203],"many":[205],"genes,":[207],"which":[209],"sizeable":[211],"number":[212],"confirmed":[214],"either":[215],"PubMed":[217],"literature":[218],"reports":[219],"electronically":[221],"interfered":[222],"annotations.":[223],"Finally,":[224],"studied":[226],"cell":[227],"cycle":[228],"protein-protein":[229],"interactions":[230],"derived":[231],"tandem":[234],"affinity":[235],"purification":[236],"experiments":[237,241],"silico":[240],"BioGRID":[244],"interactome":[245],"database":[246],"found":[248],"strong":[249],"experimental":[250],"evidence":[251],"predictions":[254],"generated":[255],"our":[257,263],"models.":[258],"results":[260],"show":[261],"that":[262,273],"approach":[264],"can":[265],"be":[266],"build":[269],"very":[270],"robust":[271],"create":[274],"integrating":[277],"features.":[283],"AVAILABILITY:":[284],"Set-based":[287],"method":[288],"implemented":[290],"Rosetta":[293],"toolkit":[294],"kernel":[295],"version":[296],"1.0.1":[297],"at:":[299],"http://rosetta.lcb.uu.se/":[300]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}