Chapter 11: Making Sense of Proteomics: Using Bioinformatics to Discover a Protein's Structure, Functions, and Interactions—References
Altschul S.F. and Koonin E.V. 1998. Iterated profile searches with PSI-BLAST—A tool for discovery in protein databases. Trends Biochem. Sci. 23: 444–447.
Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. 1997. Gapped- BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
Attwood T.K., Blythe M.J., Flower D.R., Gaulton A., Mabey J.E., Maudling N., McGregor L., Mitchell A.L., Moulton G., Paine K., and Scordis P. 2002. PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res. 30: 239–241.
Baldi P., Brunak S., Frasconi P., Soda G., and Pollastri G. 1999. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15: 937–946.
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., and Sonnhammer E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276–280.
Blaschke C., Oliveros J.C., and Valencia A. 2001. Mining functional information associated with expression arrays. Funct. Integr. Genomics 1: 256–268.
Blom N., Gammeltoft S., and Brunak S. 1999. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294: 1351–1362.
Blom N., Hansen J., Blaas D., and Brunak S. 1996. Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks. Protein Sci. 5: 2203–2216.
Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., and Yuan Y. 1998. Predicting function: From genes to genomes and back. J. Mol. Biol. 283: 707–725.
Bujnicki J.M., Elofsson A., Fischer D., and Rychlewski L. 2001. Structure prediction meta server. Bioinformatics 17: 750–751.
Bulyk M.L., Huang X., Choo Y., and Church G.M. 2001. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. 98: 7158–7163.
Claros M.G. and von Heijne G. 1994. TopPred II: An improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10: 685–686.
Conrads T.P., Anderson G.A., Veenstra T.D., Pasa-Tolic L., and Smith R.D. 2000. Utility of accurate mass tags for proteome-wide protein identification. Anal. Chem. 72: 3349–3354.
Corpet F., Servant F., Gouzy J., and Kahn D. 2000. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28: 267–269.
Cserzo M., Wallin E., Simon I., von Heijne G., and Elofsson A. 1997. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method. Protein Eng. 10: 673–676.
Cuff J.A., Clamp M.E., Siddiqui A.S., Finlay M., and Barton G.J. 1998. JPred: A consensus secondary structure prediction server. Bioinformatics 14: 892–893.
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.
Dongre A.R., Eng J.K., and Yates J.R. III. 1997. Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins. Trends Biotechnol. 15: 418–425.
Eisen J.A. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 26: 4291–4300.
Emanuelsson O., Nielsen H., and von Heijne G. 1999. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978–984.
Emanuelsson O., Nielsen H., Brunak S., and von Heijne G. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300: 1005–1016.
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.
Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., and Bairoch A. 2002. The PROSITE database, its status in 2002. Nucleic Acids Res. 30: 235–238.
Fischer D., Barret C., Bryson K., Elofsson A., Godzik A., Jones D., Karplus K.J., Kelley L.A., MacCallum R.M., Pawowski K., Rost B., Rychlewski L., and Sternberg M. 1999. CAFASP-1: Critical assessment of fully automated structure prediction methods. Proteins (suppl.) 37: 209–217.
Fitch W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99–113.
Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., and Ahringer J. 2000. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325–330.
Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., Remor M., Hofert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M.A., Copley R.R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., and Superti-Furga G. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147.
Gawantka V., Pollet N., Delius H., Vingron M., Pfister R., Nitsch R., Blumenstock C., and Niehrs C. 1998. Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech. Dev. 77: 95–141.
George R.A. and Heringa J. 2002. SnapDRAGON: A method to delineate protein structural domains from sequence data. J. Mol. Biol. 316: 839–851.
Gonczy P., Echeverri G., Oegema K., Coulson A., Jones S.J., Copley R.R., Duperon J., Oegema J., Brehm M., Cassin E., Hannak E., Kirkham M., Pichler S., Flohrs K., Goessen A., Leidel S., Alleaume A.M., Martin C., Ozlu N., Bork P., and Hyman A.A. 2000. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408: 331–336.
Gupta R., Birch H., Rapacki K., Brunak S., and Hansen J.E. 1999. O-GLYCBASE version 4.0: A revised database of O-glycosylated proteins. Nucleic Acids Res. 27: 370–372.
Gygi S.P., Rochon Y., Franza B.R., and Aebersold R. 1999a. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19: 1720–1730.
Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. 1999b. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17: 994–999.
Henikoff S., Henikoff J.G., and Pietrokovski S. 1999. Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 15: 471–479.
Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., Yang L., Wolting C., Donaldson I., Schandorff S., Shewnarane J., Vo M., Taggart J., Goudreault M., Muskat B., Alfarano C., Dewar D., Lin Z., Michalickova K., Willems A.R., Sassi H., Nielsen P.A., Rasmussen K.J., Andersen J.R., Johansen L.E., Hansen L.H., Jespersen H., Podtelejnikov A., Nielsen E., Crawford J., Poulsen V., Sorensen B.D., Matthiesen J., Hendrickson R.C., Gleeson F., Pawson T., Moran M.F., Durocher D., Mann M., Hogue C.W., Figeys D., and Tyers M. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.
Hollingsworth N.M., Ponte L., and Halsey C. 1995. MSH5, a novel MutS homolog, facilitates meiotic reciprocal recombination between homologs in Saccharomyces cerevisiae but not mismatch repair. Genes Dev. 9: 1728–1739.
Huang J.Y. and Brutlag D.L. 2001. The EMOTIF database. Nucleic Acids Res. 29: 202–204.
Humphreys K., Demetriou G., and Gaizauskas R. 2000. Two applications of information extraction to biological science journal articles: Enzyme interactions and protein structures. Pac. Symp. Biocomput. 5: 505–516.
Hutchison C.A., Peterson S.N., Gill S.R., Cline R.T., White O., Fraser C.M., Smith H.O., and Venter J.C. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165–2169.
Huynen M., Snel B., Lathe W. III, and Bork P. 2000. Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res. 10: 1204–1210.
Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929–934.
Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569–4574.
Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., and Sakaki Y. 2000. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. 97: 1143–1147.
Iyer V.R., Horak C.E., Scafe C.S., Botstein D., Snyder M., and Brown P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533–558.
Jensen P.K., Pasa-Tolic L., Peden K.K., Martinovic S., Lipton M.S., Anderson G.A., Tolic N., Wong K.K., and Smith R.D. 2000. Mass spectrometric detection for capillary isoelectric focusing separations of complex protein mixtures. Electrophoresis 21: 1372–1380.
Johnson R.E., Kovvali G.K., Prakash L., and Prakash S. 1996. Requirement of the yeast MSH3 and MSH6 genes for MSH2-dependent genomic stability. J. Biol. Chem. 271: 7285–7288.
Jones D.T. and Swindells M.B. 2002. Getting the most from PSI-BLAST. Trends Biochem. Sci. 27: 161–164.
Kanehisa M. and Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27–30.
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.
Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305: 567–580.
Maeda I., Kohara Y., Yamamoto M., and Sugimoto A. 2001. Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11: 171–176.
Marcotte E.M. 2000. Computational genetics: Finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10: 359–365.
Marcotte E.M., Xenarios I., and Eisenberg D. 2001. Mining literature for protein-protein interactions. Bioinformatics 17: 359–363.
Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., and Eisenberg D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751–753.
Matthews L.R., Vaglio P., Reboul J., Ge H., Davis B.P., Garrels J., Vincent S., and Vidal M. 2001. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11: 2120–2126.
McGuffin L.J., Bryson K., and Jones D.T. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16: 404–405.
Moller S., Croning M.D., and Apweiler R. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646–653.
Moult J., Fidelis K., Zemla A., and Hubbard T. 2001. Critical assessment of methods of protein structure prediction (CASP): Round IV. Proteins (suppl. 5) 45: 2–7.
Mount D.W. 2001. Bioinformatics: Sequencing and genome analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Nakai K. 2000. Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem. 54: 277–344.
Ouali M. and King R.D. 2000. Cascaded multiple classifiers for secondary structure prediction. Protein Sci. 9: 1162–1176.
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.
Peitsch M.C. 1996. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24: 274–279.
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.
Pieper U., Eswar N., Stuart A.C., Ilyin V.A., and Sali A. 2002. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30: 255–259.
Pollet N., Schmidt H.A., Gawantka V., Vingron M., and Niehrs C. 2000. Axeldb: A Xenopus laevis database focusing on gene expression. Nucleic Acids Res. 28: 139–140.
Proux D., Rechenmann F., and Julliard L. 2000. A pragmatic information extraction strategy for gathering data on genetic interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8: 279–285.
Rain J.C., Selig L., De Reuse H., Battaglia V., Reverdy C., Simon S., Lenzen G., Petel F., Wojcik J., Schachter V., Chemama Y., Labigne A., and Legrain P. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211–215.
Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E., Volkert T.L., Wilson C.J., Bell S.P., and Young R.A. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306–2309.
Ross-Macdonald P., Coelho P.S., Roemer T., Agarwal S., Kumar A., Jansen R., Cheung K.H., Sheehan A., Symoniatis D., Umansky L., Heidtman M., Nelson F.K., Iwasaki H., Hager K., Gerstein M., Miller P., Roeder G.S., and Snyder M. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402: 413–418.
Rost B. and Sander C. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19: 55–72.
Rost B., Fariselli P., and Casadio R. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5: 1704–1718.
Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J. 2000. Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. 97: 6652–6657.
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.
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.
Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., and Koonin E.V. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22–28.
Thomas J., Milward D., Ouzounis C., Pulman S., and Carroll M. 2000. Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput. 5: 538–549.
Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876–4882.
Thornton J.W. and DeSalle R. 2000. Gene family evolution and homology: Genomics meets phylogenetics. Annu. Rev. Genomics Hum. Genet. 1: 41–73.
Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., and Rothberg J.M. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.
Vlahovicek K., Murvai J., Barta E., and Pongor S. 2002. The SBASE protein domain library, release 9.0: An online resource for protein domain identification. Nucleic Acids Res. 30: 273–275.
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.
Wheelan S.J., Marchler-Bauer A., and Bryant S.H. 2000. Domain size distributions can predict domain boundaries. Bioinformatics 16: 613–618.
Wingender E., Chen X., Fricke E., Geffers R., Hehl R., Liebich I., Krull M., Matys V., Michael H., Ohnhauser R., Pruss M., Schacherer F., Thiele S., and Urbach S. 2001. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29: 281–283.
Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., Chu A.M., Connelly C., Davis K., Dietrich F., Dow S.W., El Bakkoury M., Foury F., Friend S.H., Gentalen E., Giaever G., Hegemann J.H., Jones T., Laub M., Liao H., Davis R.W., et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906.
Xenarios I., Salwinski L., Duan X.J., Higney P., Kim S.M., and Eisenberg D. 2002. DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303–305.
|