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Originally published In Press as doi:10.1074/mcp.M400169-MCP200 on December 15, 2004.
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Molecular & Cellular Proteomics 4:205-213, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Automated Yeast Two-hybrid Screening for Nuclear Receptor-interacting Proteins*,S

Michael Albers{ddagger}, Harald Kranz§, Ingo Kober, Carmen Kaiser||, Martin Klink**, Jörg Suckow{ddagger}{ddagger}, Rainer Kern** and Manfred Koegl{ddagger},§§

From {ddagger} PheneX Pharmaceuticals AG, Im Neuenheimer Feld 515 and § Gene Bridges GmbH, Im Neuenheimer Feld 584, 69120 Heidelberg, CADS, Merck KGaA, A46/312, Frankfurter Strasse 250, D-64293 Darmstadt, || BD Diagnostics, Tullastrasse 8-12, 69126 Heidelberg, ** LIONbioscience AG, Waldhoferstr. 98, 69123 Heidelberg, and {ddagger}{ddagger} Temis Deutschland GmbH, Kurfürstenanlage 3, D-69115 Heidelberg, Germany

High throughput analysis of protein-protein interactions is an important sector of hypothesis-generating research. Using an improved and automated version of the yeast two-hybrid system, we completed a large interaction screening project with a focus on nuclear receptors and their cofactors. A total of 425 independent yeast two-hybrid cDNA library screens resulted in 6425 potential interacting protein fragments involved in 1613 different interaction pairs. We show that simple statistical parameters can be used to narrow down the data set to a high confidence set of 377 interaction pairs where validated interactions are enriched to 61% of all pairs. Within the high confidence set, there are 64 novel proteins potentially binding to nuclear receptors or their cofactors. We discuss several examples of high interest, and we expect that communication of this huge data set will help to complement our knowledge of the protein interaction repertoire of this family of transcription factors and instigate the characterization of the various novel candidate interactors.

§§ To whom correspondence should be addressed: German Resource Center for Genome Research, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. Tel.: 49-179-135-68-09; Fax: 49-6221-42-47-04; E-mail:koegl{at}rzpd.de


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