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Chapter 41: Analysis of Genome-wide Protein Interactions Using Computational Approaches—References

Adai A.T., Date S.V., Wieland S., and Marcotte E.M. 2004. LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks. J. Mol. Biol. 340: 179–190.

Aloy P. and Russell R.B. 2004. Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 22: 1317–1321.

Andrade M.A., Ouzounis C., Sander C., Tamames J., and Valencia A. 1999a. Functional classes in the three domains of life. J. Mol. Evol. 49: 551–557.

Andrade M.A., Brown N.P., Leroy C., Hoersch S., de Daruvar A., Reich C., Franchini A., Tamames J., Valencia A., Ouzounis C., and Sander C. 1999b. Automated genome sequence analysis and annotation. Bioinformatics 15: 391–412.

Bader G.D. and Enright A.J. 2005. Biomolecular interactions and biological pathways. In Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edition (ed. A.D. Baxevanis and B.F.F. Oulette), pp. 254–280. Wiley, New York.

Bader G.D. and Hogue C.W. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.

Bader G.D., Betel D., and Hogue C.W. 2003. BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res. 31: 248–250.

Bairoch A. and Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45–48.

Ball C.A., Dolinski K., Dwight S.S., Harris M.A., Issel-Tarver L., Kasarskis A., Scafe C.R., Sherlock G., Binkley G., Jin H., et al. 2000. Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res. 28: 77–80.

Blaschke C., Andrade M.A., Ouzounis C., and Valencia A. 1999. Automatic extraction of biological information from scientific text: Protein-protein interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 60–67.

Blumenthal T. 1998. Gene clusters and polycistronic transcription in eukaryotes. Bioessays 20: 480–487.

Bono H., Ogata H., Goto S., and Kanehisa M. 1998. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8: 203–210.

Bowers P.M., Pellegrini M., Thompson M.J., Fierro J., Yeates T.O., and Eisenberg D. 2004. Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol. 5: R35.

Brazma A. and Vilo J. 2000. Gene expression data analysis. FEBS Lett. 480: 17–24.

Chen Z. and Han M. 2000. Building a protein interaction map: Research in the post-genome era. Bioessays 22: 503–506.

Costanzo M.C., Hogan J.D., Cusick M.E., Davis B.P., Fancher A.M., Hodges P.E., Kondu P., Lengieza C., Lew-Smith J.E., Lingner C., et al. 2000. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28: 73–76.

Craven M. and Kumlien J. 1999. Constructing biological knowledge bases by extracting information from text sources. Proc. Int. Conf. Intell. Syst. Mol. Biol. 77–86.

Dandekar T., Snel B., Huynen M., and Bork P. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324–328.

Date S.V. and Marcotte E.M. 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 21: 1055–1062.

Deng M.H., Mehta S., Sun F.Z., and Chen T. 2002. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 12: 1540–1548.

DeRisi J.L., Iyer V.R., and Brown P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686.

Doerks T., von Mering C., and Bork P. 2004. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res. 32: 6321–6326.

Eilbeck K., Brass A., Paton N., and Hodgman C. 1999. INTERACT: An object oriented protein-protein interaction database. Proc. Int. Conf. Intell. Syst. Mol. Biol. 7: 87–94.

Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863–14868.

Eisenberg D., Marcotte E.M., Xenarios I., and Yeates T.O. 2000. Protein function in the post-genomic era. Nature 405: 823–826.

Enault F., Suhre K., Poirot O., Abergel C., and Claverie J.M. 2003. Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. Nucleic Acids Res. 31: 3720–3722.

Enright A.J. and Ouzounis C.A. 2001. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2: RESEARCH0034.

Enright A.J., Kunin V., and Ouzounis C.A. 2003. Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31: 4632–4638.

Enright A.J., Iliopoulos I., Kyrpides N.C., and Ouzounis C.A. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86–90.

Fraser H.B., Hirsh A.E., Wall D.P., and Eisen M.B. 2004. Coevolution of gene expression among interacting proteins. Proc. Natl. Acad. Sci. 101: 9033–9038.

Galperin M.Y. and Koonin E.V. 2000. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18: 609–613.

Gelbart W.M., Crosby M., Matthews B., Rindone W.P., Chillemi J., Russo Twombly S., Emmert D., Ashburner M., Drysdale R.A., Whitfield E., et al. 1997. FlyBase: A Drosophila database. The FlyBase consortium. Nucleic Acids Res. 25: 63–66.

Goh C.S. and Cohen F.E. 2002. Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324: 177–192.

Goldovsky L., Cases I., Enright A.J., and Ouzounis C.A. 2005. Biolayoutjava: Versatile network visualization of structural and functional relationships. Appl. Bioinformatics 4: 71–74.

Grigoriev A. 2003. On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res. 31: 4157–4161.

Hermjakob H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., Vingron M., Roechert B., Roepstorff P., Valencia A., et al. 2004. IntAct: An open source molecular interaction database. Nucleic Acids Res. 32: D452–455.

Hodges P.E., McKee A.H., Davis B.P., Payne W.E., and Garrels J.I. 1999. The Yeast Proteome Database (YPD): A model for the organization and presentation of genome-wide functional data. Nucleic Acids Res. 27: 69–73.

Hu Z., Mellor J., Wu J., and DeLisi C. 2004. VisANT: An online visualization and analysis tool for biological interaction data. BMC Bioinformatics 5: 17.

Hua S.J., Guo T., Gough J., and Sun Z.R. 2002. Proteins with class α/β fold have high-level participation in fusion events. J. Mol. Biol. 320: 713–719.

Huynen M.A., Dandekar T., and Bork P. 1999. Variation and evolution of the citric-acid cycle: A genomic perspective. Trends Microbiol. 7: 281–291.

Huynen M., Snel B., Lathe W., and Bork P. 2000a. Exploitation of gene context. Curr. Opin. Struct. Biol. 10: 366–370.

Huynen M., Snel B., Lathe W., and Bork P. 2000b. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res. 10: 1204–1210.

Igarashi T. and Kaminuma T. 1997. Development of a cell signaling networks database. Pac. Symp. Biocomput. 187–197.

Iliopoulos I., Enright A.J., and Ouzounis C.A. 2001. TextQuest: Document clustering of MedLine abstracts for concept discovery in molecular biology. Pac. Symp. Biocomput. 8: 6384–6395.

Iliopoulos I., Enright A.J., Poullet P., and Ouzounis C.A. 2003. Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis. Comp. Funct. Genomics 4: 337–341.

Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., Emili A., Snyder M., Greenblatt J.F., and Gerstein M. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449–453.

Jim K., Parmar K., Singh M., and Tavazoie S. 2004. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res. 14: 109–115.

Kanehisa M. and Goto S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28: 27–30.

Karp P.D. 2000. An ontology for biological function based on molecular interactions. Bioinformatics 16: 269–285.

Karp P.D., Ouzounis C., and Paley S. 1996. HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae. Proc. Int. Conf. Intell. Syst. Mol. Biol. 4: 116–124.

Karp P.D., Riley M., Saier M., Paulsen I.T., Paley S.M., and Pellegrini-Toole A. 2000. The EcoCyc and MetaCyc databases. Nucleic Acids Res. 28: 56–59.

Kryukov G.V., Kumar R.A., Koc A., Sun Z.H., and Gladyshev V.N. 2002. Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase. Proc. Natl. Acad. Sci. 99: 4245–4250.

Kyrpides N.C., Ouzounis C.A., Iliopoulos I., Vonstein V., and Overbeek R. 2000. Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. Nucleic Acids Res. 28: 4573–4576.

Legrain P. and Selig L. 2000. Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 480: 32–36.

Lehner B. and Fraser A.G. 2004. A first-draft human protein-interaction map. Genome Biol. 5: R63.

Levesque M., Shasha D., Kim W., Surette M.G., and Benfey P.N. 2003. Trait-to-gene: A computational method for predicting the function of uncharacterized genes. Curr. Biol. 13: 129–133.

Lewis S., Ashburner M., and Reese M.G. 2000. Annotating eukaryotic genomes. Curr. Opin. Struct. Biol. 10: 349–354.

Marcotte E.M. 2000. Computational genetics: Finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10: 359–365.

Marcotte E.M., Xenarios I., van Der Bliek A.M., and Eisenberg D. 2000. Localizing proteins in the cell from their phylogenetic profiles. Proc. Natl. Acad. Sci. 97: 12115–12120.

Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., and Eisenberg D. 1999a. A combined algorithm for genome-wide prediction of protein function. Nature 402: 83–86.

Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., and Eisenberg D. 1999b. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751–753.

Mellor J.C., Yanai I., Clodfelter K.H., Mintseris J., and DeLisi C. 2002. Predictome: A database of putative functional links between proteins. Nucleic Acids Res. 30: 306–309.

Morett E., Korbel J.O., Rajan E., Saab-Rincon G., Olvera L., Olvera M., Steffen S., Snel B., and Bork P. 2003. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat. Biotechnol. 21: 790–795.

Mushegian A.R. and Koonin E.V. 1996. Gene order is not conserved in bacterial evolution. Trends Genet. 12: 289–290.

Nierman W.C., Eisen J.A., Fleischmann R.D., and Fraser C.M. 2000. Genome data: What do we learn? Curr. Opin. Struct. Biol. 10: 343–348.

Ouzounis C. 1999. Orthology: Another terminology muddle. Trends Genet. 15: 445–445.

Ouzounis C.A. and Karp P.D. 2000. Global properties of the metabolic map of Escherichia coli. Genome Res. 10: 568–576.

Ouzounis C. and Kyrpides N. 1996. The emergence of major cellular processes in evolution. FEBS Lett. 390: 119–123.

Ouzounis C.A., Coulson R.M.R., Enright A.J., Kunin V., and Pereira-Leal J.B. 2003. Classification schemes for protein structure and function. Nat. Rev. Genet. 4: 508–519.

Overbeek R., Fonstein M., D'Souza M., Pusch G.D., and Maltsev N. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. 96: 2896–2901.

Overbeek R., Larsen N., Pusch G.D., D'Souza M., Selkov E., Jr., Kyrpides N., Fonstein M., Maltsev N., and Selkov E. 2000. WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28: 123–125.

Pazos F. and Valencia A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14: 609–614.

Pazos F. and Valencia A. 2002. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219–227.

Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O. 1999. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. 96: 4285–4288.

Pereira-Leal J.B., Enright A.J., and Ouzounis C.A. 2004. Detection of functional modules from protein interaction networks. Proteins 54: 49–57.

Ramani A.K. and Marcotte E.M. 2003. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327: 273–284.

Rivera M.C., Jain R., Mooer J.E., and Lake J.A. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. 95: 6239–6244.

Ross D.T., Scherf U., Eisen M.B., Perou C.M., Rees C., Spellman P., Iyer V., Jeffrey S.S., Van de Rijn M., Waltham M., et al. 2000. Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet. 24: 227–235.

Selkov E., Overbeek R., Kogan Y., Chu L., Vonstein V., Holmes D., Silver S., Haselkorn R., and Fonstein M. 2000. Functional analysis of gapped microbial genomes: Amino acid metabolism of Thiobacillus ferrooxidans. Proc. Natl. Acad. Sci. 97: 3509–3514.

Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., and Ideker T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498–2504.

Snel B., Bork P., and Huynen M.A. 2002. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. 99: 5890–5895.

Snel B., Lehmann G., Bork P., and Huynen M.A. 2000. STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28: 3442–3444.

Spirin V. and Mirny L.A. 2003. Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. 100: 12123–12128.

Sprinzak E. and Margalit H. 2001. Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311: 681–692.

Stapley B.J. and Benoit G. 2000. Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac. Symp. Biocomput. 529–540.

Strong M., Graeber T.G., Beeby M., Pellegrini M., Thompson M.J., Yeates T.O., and Eisenberg D. 2003. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 31: 7099–7109.

Tamames J., Casari G., Ouzounis C., and Valencia A. 1997. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44: 66–73.

Tamames J., Ouzounis C., Sander C., and Valencia A. 1996. Genomes with distinct function composition. FEBS Lett. 389: 96–101.

Tatusov R.L., Koonin E.V., and Lipman D.J. 1997. A genomic perspective on protein families. Science 278: 631–637.

Tatusov R.L., Mushegian A.R., Bork P., Brown N.P., Hayes W.S., Borodovsky M., Rudd K.E., and Koonin E.V. 1996. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol. 6: 279–291.

Thomas J., Milward D., Ouzounis C., Pulman S., and Carroll M. 2000. Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput. 541–552.

Tsoka S. and Ouzounis C.A. 2000a. Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion. Nat. Genet. 26: 141–142.

Tsoka S. and Ouzounis C.A. 2000b. Recent developments and future directions in computational genomics. FEBS Lett. 480: 42–48.

von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P., and Snel B. 2003a. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258–261.

von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., and Bork P. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399–403.

von Mering C., Zdobnov E.M., Tsoka S., Ciccarelli F.D., Pereira-Leal J.B., Ouzounis C.A., and Bork P. 2003b. Genome evolution reveals biochemical networks and functional modules. Proc. Natl. Acad. Sci. 100: 15428–15433.

Wong S.L., Zhang L.V., Tong A.H., Li Z., Goldberg D.S., King O.D., Lesage G., Vidal M., Andrews B., Bussey H., Boone C., and Roth F.P. 2004. Combining biological networks to predict genetic interactions. Proc. Natl. Acad. Sci. 101: 15682–15687.

Wu J., Kasif S., and DeLisi C. 2003. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19: 1524–1530.

Xenarios I., Rice D.W., Salwinski L., Baron M.K., Marcotte E.M., and Eisenberg D. 2000. DIP: The database of interacting proteins. Nucleic Acids Res. 28: 289–291.

Yanai I., Derti A., and DeLisi C. 2001. Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. 98: 7940–7945.

Zorio D.A., Cheng N.N., Blumenthal T., and Spieth J. 1994. Operons as a common form of chromosomal organization in C. elegans. Nature 372: 270–272.

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