{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,29]],"date-time":"2025-11-29T10:48:32Z","timestamp":1764413312974},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Systems biology attempts to describe complex systems behaviors in terms of dynamic operations of biological networks. However, there is lack of tools that can effectively decode complex network dynamics over multiple conditions.<\/jats:p>\n               <jats:p>Results: We present principal network analysis (PNA) that can automatically capture major dynamic activation patterns over multiple conditions and then generate protein and metabolic subnetworks for the captured patterns. We first demonstrated the utility of this method by applying it to a synthetic dataset. The results showed that PNA correctly captured the subnetworks representing dynamics in the data. We further applied PNA to two time-course gene expression profiles collected from (i) MCF7 cells after treatments of HRG at multiple doses and (ii) brain samples of four strains of mice infected with two prion strains. The resulting subnetworks and their interactions revealed network dynamics associated with HRG dose-dependent regulation of cell proliferation and differentiation and early PrPSc accumulation during prion infection.<\/jats:p>\n               <jats:p>Availability: The web-based software is available at: http:\/\/sbm.postech.ac.kr\/pna.<\/jats:p>\n               <jats:p>Contact: \u00a0dhhwang@postech.ac.kr; seungjin@postech.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq670","type":"journal-article","created":{"date-parts":[[2010,12,31]],"date-time":"2010-12-31T01:59:43Z","timestamp":1293760783000},"page":"391-398","source":"Crossref","is-referenced-by-count":47,"title":["Principal network analysis: identification of subnetworks representing major dynamics using gene expression data"],"prefix":"10.1093","volume":"27","author":[{"given":"Yongsoo","family":"Kim","sequence":"first","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Taek-Kyun","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Yungu","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Jiho","family":"Yoo","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Sungyong","family":"You","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Inyoul","family":"Lee","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"George","family":"Carlson","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Leroy","family":"Hood","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Seungjin","family":"Choi","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"},{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]},{"given":"Daehee","family":"Hwang","sequence":"additional","affiliation":[{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"},{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"},{"name":"1 School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 2Department of Computer Science and Engineering, POSTECH, Pohang, Republic of Korea, 3Institute for Systems Biology, Seattle, 4McLaughlin Research Institute, Great Falls, USA, 5Division of IT Convergence Engineering, POSTECH, 6Division of Integrative Biosciences and Biotechnology, POSTECH and 7Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea"}]}],"member":"286","published-online":{"date-parts":[[2010,12,30]]},"reference":[{"key":"2023012511535460800_B1","first-page":"10","article-title":"Clustering and metaclustering with nonnegtaive matrix decompositions","volume-title":"Proceedings of the European Conference on Machine 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