{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T18:45:34Z","timestamp":1778352334704,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1778,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights.<\/jats:p>\n               <jats:p>Results: We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples.<\/jats:p>\n               <jats:p>Availability: \u00a0Supplementary data and source code are available from http:\/\/www.ebi.ac.uk\/fg\/research\/rex.<\/jats:p>\n               <jats:p>Contact: \u00a0samuel.kaski@aalto.fi<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr634","type":"journal-article","created":{"date-parts":[[2011,11,22]],"date-time":"2011-11-22T04:39:50Z","timestamp":1321936790000},"page":"246-253","source":"Crossref","is-referenced-by-count":14,"title":["Data-driven information retrieval in heterogeneous collections of transcriptomics data links <i>SIM2s<\/i> to malignant pleural mesothelioma"],"prefix":"10.1093","volume":"28","author":[{"given":"Jos\u00e9","family":"Caldas","sequence":"first","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nils","family":"Gehlenborg","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"},{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eeva","family":"Kettunen","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali","family":"Faisal","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikko","family":"R\u00f6nty","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew G.","family":"Nicholson","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sakari","family":"Knuutila","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, 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