{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:14:54Z","timestamp":1773288894206,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein-protein interaction (PPI) databases are widely used tools to study cellular pathways and networks; however, there are several databases available that still do not account for cell type-specific differences. Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature are involved in good quality interactions.<\/jats:p>\n               <jats:p>Results: We found that the evaluated databases are comparable in terms of node connectivity (i.e. proteins with few interaction partners also have few interaction partners in other databases), but may differ in the identity of interaction partners. We also observed that the incorporation of tissue-specific expression information significantly altered the interaction landscape and finally, we demonstrated that many of the most intensively studied proteins are engaged in interactions associated with low confidence scores. In summary, interaction databases are valuable research tools but may lead to different predictions on interactions or pathways. The accuracy of predictions can be improved by incorporating datasets on organ- and cell type-specific gene expression, and by obtaining additional interaction evidence for the most \u2018popular\u2019 proteins.<\/jats:p>\n               <jats:p>Contact: \u00a0kitano@sbi.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr414","type":"journal-article","created":{"date-parts":[[2011,7,29]],"date-time":"2011-07-29T01:30:44Z","timestamp":1311903044000},"page":"2414-2421","source":"Crossref","is-referenced-by-count":41,"title":["Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases"],"prefix":"10.1093","volume":"27","author":[{"given":"Tiago J. S.","family":"Lopes","sequence":"first","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Martin","family":"Schaefer","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Jason","family":"Shoemaker","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Yukiko","family":"Matsuoka","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Jean\u2212Fred","family":"Fontaine","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Gabriele","family":"Neumann","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Miguel A.","family":"Andrade-Navarro","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Yoshihiro","family":"Kawaoka","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"}]},{"given":"Hiroaki","family":"Kitano","sequence":"additional","affiliation":[{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan"},{"name":"1 JST ERATO KAWAOKA Infection\u2212induced Host Responses Project, Tokyo, Japan, 2Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, Berlin, Germany, 3The Systems Biology Institute, Tokyo, Japan, 4Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, School of Veterinary Medicine, Madison, WI, USA, 5Institute of Medical Science, Division of Virology, Department of Microbiology and Immunology, University of Tokyo, 6Sony Computer Science Laboratories, Inc., Tokyo, 7Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa and 8Division of Cancer Systems Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 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