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Part of the book series: Computational Biology ((COBO,volume 24))

Abstract

This chapter provides an overview of key topics that serve as background for the rest of the book. First, we discuss the roles of proteins in living organisms.

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References

  1. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, Gene Ontology: tool for the unification of biology. the Gene Ontology consortium. Nat. Genet. 25, 25–29 (2000)

    Article  Google Scholar 

  2. G.D. Bader, I. Donaldson, C. Wolting, B.F. Ouellette, T. Pawson, C.W. Hogue, BIND-the biomolecular interaction network database. Nucl. Acids Res. 29, 242–245 (2001)

    Article  Google Scholar 

  3. T. Beissbarth, T.P. Speed, GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (Oxford, England) 20, 1464–1465 (2004)

    Article  Google Scholar 

  4. Biocarta, BioCarta

    Google Scholar 

  5. P. Braun, M. Tasan, M. Dreze, M. Barrios-Rodiles, I. Lemmens, H. Yu, J.M. Sahalie, R.R. Murray, L. Roncari, A.-S. de Smet, K. Venkatesan, J.-F. Rual, J. Vandenhaute, M.E. Cusick, T. Pawson, D.E. Hill, J. Tavernier, J.L. Wrana, F.P. Roth, M. Vidal, An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91–97 (2009)

    Article  Google Scholar 

  6. E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, D. Binns, N. Harte, R. Lopez, R. Apweiler, The Gene Ontology annotation (GOA) database: sharing knowledge in uniprot with Gene Ontology. Nucl. Acids Res. 32, D262–D266 (2004)

    Article  Google Scholar 

  7. F. Crick, Central dogma of molecular biology. Nature 227, 561–563 (1970)

    Article  Google Scholar 

  8. H. Dinkel, C. Chica, A. Via, C.M. Gould, L.J. Jensen, T.J. Gibson, F. Diella, Phospho.ELM: a database of phosphorylation sites-update 2011. Nucl. Acids Res. 39, D261–D267 (2011)

    Article  Google Scholar 

  9. S.W. Doniger, N. Salomonis, K.D. Dahlquist, K. Vranizan, S.C. Lawlor, B.R. Conklin, MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Gen. Biol. 4, R7–R7 (2003)

    Article  Google Scholar 

  10. F. Gnad, S. Ren, J. Cox, J.V. Olsen, B. Macek, M. Oroshi, M. Mann, PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Gen. Biol. 8, R250–D250 (2007)

    Article  Google Scholar 

  11. A. Hamosh, A.F. Scott, J.S. Amberger, C.A. Bocchini, V.A. McKusick, Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucl. Acids Res. 33, D514–D517 (2005)

    Article  Google Scholar 

  12. M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G.M. Rubin, J.A. Blake, C. Bult, M. Dolan, H. Drabkin, J.T. Eppig, D.P. Hill, L. Ni, M. Ringwald, R. Balakrishnan, J.M. Cherry, K.R. Christie, M.C. Costanzo, S.S. Dwight, S. Engel, D.G. Fisk, J.E. Hirschman, E.L. Hong, R.S. Nash, A. Sethuraman, C.L. Theesfeld, D. Botstein, K. Dolinski, B. Feierbach, T. Berardini, S. Mundodi, S.Y. Rhee, R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee, R. Chisholm, P. Gaudet, W. Kibbe, R. Kishore, E.M. Schwarz, P. Sternberg, M. Gwinn, L. Hannick, J. Wortman, M. Berriman, V. Wood, N. de la Cruz, P. Tonellato, P. Jaiswal, T. Seigfried, R. White, The Gene Ontology (GO) database and informatics resource. Nucl. Acids Res. 32, D258–D261 (2004)

    Google Scholar 

  13. H. Huang, J.S. Bader, Precision and recall estimates for two-hybrid screens. Bioinformatics (Oxford, England) 25, 372–378 (2009)

    Article  Google Scholar 

  14. D.W. Huang, B.T. Sherman, R.A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009)

    Article  Google Scholar 

  15. L.A. Huber, Is proteomics heading in the wrong direction? Nat. Rev. Mol. Cell Biol. 4, 74–80 (2003)

    Article  Google Scholar 

  16. C.-D. Hu, Y. Chinenov, T.K. Kerppola, Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell 9, 789–798 (2002)

    Article  Google Scholar 

  17. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, Y. Sakaki, A comprehensive two-hybrid analysis to explore the yeast protein interactome. in Proceedings of the National Academy of Sciences of the United States of America, vol. 98 (2001), pp. 4569–4574

    Google Scholar 

  18. G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D’Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, L. Matthews, S. Lewis, E. Birney, L. Stein, Reactome: a knowledgebase of biological pathways. Nucl. Acids Res. 33, D428–D432 (2005)

    Article  Google Scholar 

  19. M. Kanehisa, S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 28, 27–30 (2000)

    Article  Google Scholar 

  20. P.D. Karp, C.A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahrén, S. Tsoka, N. Darzentas, V. Kunin, N. López-Bigas, Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucl. Acids Res. 33, 6083–6089 (2005)

    Article  Google Scholar 

  21. S. Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, L. Montecchi-Palazzi, S. Orchard, J. Risse, K. Robbe, B. Roechert, D. Thorneycroft, Y. Zhang, R. Apweiler, H. Hermjakob, IntAct-open source resource for molecular interaction data. Nucl. Acids Res. 35, D561–D565 (2007)

    Article  Google Scholar 

  22. W.H. Landschulz, P.F. Johnson, S.L. McKnight, The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science (New York, N.Y.) 240, 1759–1764 (1988)

    Article  Google Scholar 

  23. J. Lodish, H.F. Baltimore, D. Berk, A. Darnell, Molecular Cell Biology (WH Freeman, New York, 1995)

    Google Scholar 

  24. V. Marshansky, M. Futai, The V-type H+-ATPase in vesicular trafficking: targeting, regulation and function. Curr. Opin. Cell Biol. 20, 415–426 (2008)

    Article  Google Scholar 

  25. I.M.A. Nooren, J.M. Thornton, Diversity of protein-protein interactions. EMBO J. 22, 3486–3492 (2003)

    Article  Google Scholar 

  26. P. Pagel, S. Kovac, M. Oesterheld, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, P. Mark, V. Stümpflen, H.-W. Mewes, A. Ruepp, D. Frishman, The MIPS mammalian protein-protein interaction database. Bioinformatics (Oxford, England) 21, 832–834 (2005)

    Google Scholar 

  27. S. Peri, J.D. Navarro, R. Amanchy, T.Z. Kristiansen, C.K. Jonnalagadda, V. Surendranath, V. Niranjan, B. Muthusamy, T.K.B. Gandhi, M. Gronborg, N. Ibarrola, N. Deshpande, K. Shanker, H.N. Shivashankar, B.P. Rashmi, M.A. Ramya, Z. Zhao, K.N. Chandrika, N. Padma, H.C. Harsha, A.J. Yatish, M.P. Kavitha, M. Menezes, D.R. Choudhury, S. Suresh, N. Ghosh, R. Saravana, S. Chandran, S. Krishna, M. Joy, S.K. Anand, V. Madavan, A. Joseph, G.W. Wong, W.P. Schiemann, S.N. Constantinescu, L. Huang, R. Khosravi-Far, H. Steen, M. Tewari, S. Ghaffari, G.C. Blobe, C.V. Dang, J.G.N. Garcia, J. Pevsner, O.N. Jensen, P. Roepstorff, K.S. Deshpande, A.M. Chinnaiyan, A. Hamosh, A. Chakravarti, A. Pandey, Development of human protein reference database as an initial platform for approaching systems biology in humans. Gen. Res. 13, 2363–2371 (2003)

    Article  Google Scholar 

  28. O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, B. Séraphin, The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods (San Diego, Calif.) 24, 218–229 (2001)

    Article  Google Scholar 

  29. B. Raghavachari, A. Tasneem, T.M. Przytycka, R. Jothi, DOMINE: a database of protein domain interactions. Nucl. Acids Res. 36, D656–D661 (2008)

    Article  Google Scholar 

  30. G. Scatchard, The attractions of proteins for small molecules and ions. Ann. New York Acad. Sci. 51, 660–672 (1949)

    Article  Google Scholar 

  31. H. Schägger, Tricine-SDS-PAGE. Nat. Protoc. 1, 16–22 (2006)

    Article  Google Scholar 

  32. C. Stark, B.-J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, M. Tyers, BioGRID: a general repository for interaction datasets. Nucl. Acids Res. 34, D535–D539 (2006)

    Article  Google Scholar 

  33. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, J.P. Mesirov, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. in Proceedings of the National Academy of Sciences of the United States of America, vol. 102 (2005), pp. 15545–15550

    Google Scholar 

  34. D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, T. Doerks, M. Stark, J. Muller, P. Bork, L.J. Jensen, C. von Mering, The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucl. Acids Res. 39, D561–D568 (2011)

    Article  Google Scholar 

  35. I. Xenarios, D.W. Rice, L. Salwinski, M.K. Baron, E.M. Marcotte, D. Eisenberg, DIP: the database of interacting proteins. Nucl. Acids Res. 28, 289–291 (2000)

    Article  Google Scholar 

  36. T.S. Young, P.G. Schultz, Beyond the canonical 20 amino acids: expanding the genetic lexicon. J. Biol. Chem. 285, 11039–11044 (2010)

    Article  Google Scholar 

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Correspondence to Sourav S. Bhowmick .

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Bhowmick, S.S., Seah, BS. (2017). Background. In: Summarizing Biological Networks. Computational Biology, vol 24. Springer, Cham. https://doi.org/10.1007/978-3-319-54621-6_2

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  • DOI: https://doi.org/10.1007/978-3-319-54621-6_2

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