© 1999 Macmillan Magazines Ltdletters to nature86 NATURE|VOL 402|4 NOVEMBER 1999|www.nature.comCalculation of correlated mRNA expressionResults of 97 individual publicly available DNA chip yeast mRNA expression data sets22±25were encoded as a string of 97 numbers associated with each yeast open reading frame(ORF) describing how the mRNA of that ORF changed levels during normal growth,glucose starvation, sporulation and expression of mutant genes. This string is the analoguewithin one organism of a phylogenetic pro®le1. The mRNA levels for each of the 97experiments were normalized, and only genes that showed a two-standard-deviationchange from the mean in at least one experiment were accepted, thereby ignoring genesthat showed no change in expression levels for any experiment. Open reading frames withcorrelated expression patterns were grouped together by calculating the 97-dimensionaleuclidean distance that describes the similarity in mRNA expression patterns. Openreading frames were considered to be linked if they were among the 10 closest neighbourswithin a given distance cut-off, conditions that maximized the overlap of ORF annotationbetween neighbours.Calculation of domain fusionsProteins were linked by Rosetta Stone patterns as in ref. 3. Alignments were found with theprogram PSI-BLAST21. MReceived 7 May; accepted 23 August 1999.1. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. Assigning proteinfunctions by comparative genome analysis: protein phylogenetic pro®les. Proc. Natl Acad. Sci. USA 96,4285±4288 (1999).2. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wideexpression patterns. Proc. Natl Acad. Sci. USA 95, 14863±14868 (1998).3. Marcotte, E. M. et al. Detecting protein function and protein±protein interactions from genomesequences. Science 285, 751±753 (1999).4. Mewes, H. W., Hani, J., Pfeiffer, F. & Frishman, D. MIPS: a database for protein sequences andcomplete genomes. Nucleic Acids Res. 26, 33±37 (1998).5. Karp, P., Riley, M., Paley, S. & Pellegrini-Toole, A. EcoCyc: Encyclopedia of Escherichia coli genes andmetabolism. Nucleic Acids Res. 26, 50±53 (1998).6. The yeast genome directory. Nature 387 (suppl), 1±105 (1997).7. Bairoch, A. & Apewiler, R. The SWISS-PROT protein sequence data bank and its supplement TrEMBLin 1999. Nucleic Acids Res. 27, 49±54 (1999).8. Bardosi, A., Eber, S. W., Hendrys, M. & Pekrun, A. Myopathy with altered mitochondria due to atriosephosphate isomerase (TPI) de®ciency. Acta Neuropathol. (Berl.) 79, 387±394 (1990).9. Wickner, R. B. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomycescerevisiae. Science 264, 566±569 (1994).10. Miyaki, M. et al. Germline mutation of MSH6 as the cause of hereditary nonpolyposis colorectalcancer. Nature Struct. Biol. 17, 271±272 (1997).11. Fishel, R. et al. The human mutator gene homologue MSH2 and its association with hereditarynonpolyposis colon cancer. Cell 75, 1027±1038 (1993).12. Kushirov, V. V. et al. Nucleotide sequence of the Sup2(Sup35) gene of Saccharomyces cerevisiae. Gene66, 45±54 (1988).13. Stans®eld, I. et al. The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translationtermination in Saccharomyces cerevisiae. EMBO J. 14, 4365±4373 (1995).14. Chen, X., Sullivan, D. S. & Huffaker, T. C. Two yeast genes with similarity to TCP-1 are required formicrotubule and actin function in vivo. Proc. Natl Acad. Sci. USA 91, 9111±9115 (1994).15. Johnson, R. E., Kovvali, G. K., Prakash, L. & Prakash, S. Requirement of the yeast MSH3 and MSH6genes for MSH2-dependent genomic stability. J. Biol. Chem. 271, 7285±7288 (1996).16. Lynch, H. T., Fusaro, R. M. & Lynch, J. F. Cancer genetics in the new era of molecular biology. Ann. NYAcad. Sci. 833, 1±28 (1997).17. Papadopolous, N. et al. Mutations of a MutL homolog in hereditary colon cancer. Science 263, 1625±1629 (1994).18. West, M. G., Horne, D. W. & Appling, D. R. Metabolic role of cytoplasmic isozymes of 5,10-methylenetetrahydrofolate dehydrogenase in Saccharomyces cerevisiae. Biochemistry 35, 3122±3132(1996).19. Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a ®ngerprint of proteinsthat physically interact. Trends Biochem. Sci. 23, 324±328 (1998).20. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. & Maltsev, N. The use of gene clusters to inferfunctional coupling. Proc. Natl Acad. Sci. USA 96, 2896±2901 (1999).21. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database searchprograms. Nucleic Acids Res. 25, 3389±3402 (1997).22. Spellman, P. T. et al. Comprehensive identi®cation of cell cycle-regulated genes of the yeastSaccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273±3297 (1998).23. DeRisi, J. L., Iyer, V. R. & Brown, P. O Exploring the metabolic and genetic control of gene expressionon a genomic scale. Science 278, 680±686 (1998).24. Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699±705(1998).25. Myers, L. C., Gustafsson, C. M., Hayashibara, K. C., Brown, P. O. & Kornberg, R. D. Mediator proteinmutations that selectively abolish activated transcription. Proc. Natl Acad. Sci. USA 96, 67±72 (1999).26. Horton, P. & Nakai, K. Better prediction of protein cellular localization sites with the k nearestneighbors classi®er. Intell. Sys. Molec. Biol. 5, 147±152 (1997).AcknowledgementsThis work was supported by a Department of Energy/Oak Ridge Institute for Science andEducation Hollaender postdoctoral Fellowship (E.M.), a Sloan Foundation/Departmentof Energy postdoctoral fellowship (M.P.), and grants from the DOE.Correspondence and requests for materials should be addressed to D.E.(e-mail: [email protected])..................................................................Protein interaction maps for completegenomes based on gene fusion eventsAnton J. Enright, Ioannis Iliopoulos, Nikos C. Kyrpides*& Christos A. OuzounisComputational Genomics Group, Research Programme, The EuropeanBioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD,UK* Integrated Genomics Inc., 2201 West Campbell Park Drive, Chicago,Illinois 60612, USA..............................................................................................................................................A large-scale effort to measure, detect and analyse protein±protein interactions using