{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:17:34Z","timestamp":1764688654663},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Pancreatic ductal adenocarcinoma (PDAC) eludes early detection and is characterized by its aggressiveness and resistance to current therapies. A number of gene expression screens have been carried out to identify genes differentially expressed in cancerous tissue. To identify molecular markers and suitable targets, these genes have been mapped to protein interactions to gain an understanding at systems level.<\/jats:p>\n               <jats:p>Results: Here, we take such a network-centric approach to pancreas cancer by re-constructing networks from known interactions and by predicting novel protein interactions from structural templates. The pathways we find to be largely affected are signal transduction, actin cytoskeleton regulation, cell growth and cell communication.<\/jats:p>\n               <jats:p>Our analysis indicates that the alteration of the calcium pathway plays an important role in pancreas-specific tumorigenesis. Furthermore, our structural prediction method identifies 40 novel interactions including the tissue factor pathway inhibitor 2 (TFPI2) interacting with the transmembrane protease serine 4 (TMPRSS4). Since TMPRSS4 is involved in metastasis formation, we hypothezise that the upregulation of TMPRSS4 and the downregulation of its predicted inhibitor TFPI2 plays an important role in this process. Moreover, we examine the potential role of BVDU (RP101) as an inhibitor of TMPRSS4. BDVU is known to support apoptosis and prevent the acquisition of chemoresistance. Our results suggest that BVDU might bind to the active site of TMPRSS4, thus reducing its assistance in metastasis.<\/jats:p>\n               <jats:p>Contact: ms@biotec.tu-dresden.de<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available atBioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm188","type":"journal-article","created":{"date-parts":[[2007,7,23]],"date-time":"2007-07-23T16:13:46Z","timestamp":1185207226000},"page":"i115-i124","source":"Crossref","is-referenced-by-count":15,"title":["Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data"],"prefix":"10.1093","volume":"23","author":[{"given":"Gihan","family":"Dawelbait","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"Christof","family":"Winter","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"Yanju","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"Christian","family":"Pilarsky","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"Robert","family":"Gr\u00fctzmann","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"J\u00f6rg-Christian","family":"Heinrich","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]},{"given":"Michael","family":"Schroeder","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Biotechnological Centre, TU Dresden, Dresden, Germany, 2Department of Visceral-, Thoracic- and Vascular Surgery, University Hospital, Dresden, Germany and 3RESprotect GmbH, Dresden, Germany"}]}],"member":"286","published-online":{"date-parts":[[2007,7,1]]},"reference":[{"key":"2023062708443562200_B1","doi-asserted-by":"crossref","first-page":"9067","DOI":"10.1073\/pnas.0402932101","article-title":"High-resolution characterization of the pancreatic adenocarcinoma genome","volume":"101","author":"Aguirre","year":"2004","journal-title":"Proc. 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Oncol"},{"key":"2023062708443562200_B43","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1097\/01.mpa.0000202937.55460.0c","article-title":"Hedgehog signaling in the normal and diseased pancreas","volume":"32","author":"Kayed","year":"2006","journal-title":"Pancreas"},{"key":"2023062708443562200_B44","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1093\/bioinformatics\/bth053","article-title":"Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)","volume":"20","author":"Kim","year":"2004","journal-title":"Bioinformatics"},{"key":"2023062708443562200_B45","doi-asserted-by":"crossref","first-page":"D550","DOI":"10.1093\/nar\/gkl912","article-title":"CYCLONET\u2013an integrated database on cell cycle regulation and carcinogenesis","volume":"35","author":"Kolpakov","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023062708443562200_B46","doi-asserted-by":"crossref","first-page":"6938","DOI":"10.1038\/sj.onc.1204847","article-title":"A novel function of tissue factor pathway inhibitor-2 (TFPI-2) in human glioma invasion","volume":"20","author":"Konduri","year":"2001","journal-title":"Oncogene"},{"key":"2023062708443562200_B47","first-page":"72403","article-title":"Molecular target-based therapy of pancreatic cancer","volume":"766","author":"Lebedeva","year":"2006","journal-title":"Cancer Res"},{"key":"2023062708443562200_B48","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1126\/science.1091403","article-title":"A map of the interactome network of the metazoan C. elegans","volume":"303","author":"Li","year":"2004","journal-title":"Science"},{"key":"2023062708443562200_B49","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1016\/j.str.2004.08.013","article-title":"The crystal structure of human CDK7 and its protein recognition properties","volume":"12","author":"Lolli","year":"2004","journal-title":"Structure"},{"key":"2023062708443562200_B50","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","article-title":"Comparative protein structure modeling of genes and genomes","volume":"29","author":"Mart-Renom","year":"2000","journal-title":"Annu. 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Cancer"},{"key":"2023062708443562200_B53","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1593\/neo.07103","article-title":"Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model","volume":"9","author":"Mertz","year":"2007","journal-title":"Neoplasia"},{"key":"2023062708443562200_B54","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures","volume":"247","author":"Murzin","year":"1995","journal-title":"J. Mol. 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Natl Acad. Sci. USA"},{"key":"2023062708443562200_B58","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res"},{"key":"2023062708443562200_B59","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"J. Comput. 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