string a database of predicted functional associations….pdf

STRING: a database of predicted functional associations between proteins Christian von Mering 1,2, Martijn Huynen 3, Daniel Jaeggi 1,2, Steffen Schmidt 1,2 , Peer Bork 1,2, *and Berend Snel 3 1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2Max-Delbru ¨ck-Centre for Molecular Medicine, Robert-Ro ¨ssle-Strasse 10, 13092 Berlin, Germany and 3Nijmegen Centre for Molecular Life Sciences p/a Centre of Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED Nijmegen, herlands Received August 14, 2002; Accepted September 11, 2002 ABSTRACT Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar species coverage, are often located in close proximity on the genome (in prokaryotes), and tend to be involved in gene-fusion events. The database STRING is a puted global resource for the exploration and analysis of these associations. Since the three types of evidence differ conceptually, and the number of predicted interactions is very large, it is essential to be able to assess pare the signi?cance of individual predictions. Thus, STRING contains a unique scoring-framework based on benchmarks of the different types of associations against mon reference set, inte- grated in a single con?dence score per predi