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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
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)
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)
T. Beissbarth, T.P. Speed, GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (Oxford, England) 20, 1464–1465 (2004)
Biocarta, BioCarta
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)
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)
F. Crick, Central dogma of molecular biology. Nature 227, 561–563 (1970)
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)
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)
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)
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)
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)
H. Huang, J.S. Bader, Precision and recall estimates for two-hybrid screens. Bioinformatics (Oxford, England) 25, 372–378 (2009)
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)
L.A. Huber, Is proteomics heading in the wrong direction? Nat. Rev. Mol. Cell Biol. 4, 74–80 (2003)
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)
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
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)
M. Kanehisa, S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 28, 27–30 (2000)
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)
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)
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)
J. Lodish, H.F. Baltimore, D. Berk, A. Darnell, Molecular Cell Biology (WH Freeman, New York, 1995)
V. Marshansky, M. Futai, The V-type H+-ATPase in vesicular trafficking: targeting, regulation and function. Curr. Opin. Cell Biol. 20, 415–426 (2008)
I.M.A. Nooren, J.M. Thornton, Diversity of protein-protein interactions. EMBO J. 22, 3486–3492 (2003)
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)
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)
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)
B. Raghavachari, A. Tasneem, T.M. Przytycka, R. Jothi, DOMINE: a database of protein domain interactions. Nucl. Acids Res. 36, D656–D661 (2008)
G. Scatchard, The attractions of proteins for small molecules and ions. Ann. New York Acad. Sci. 51, 660–672 (1949)
H. Schägger, Tricine-SDS-PAGE. Nat. Protoc. 1, 16–22 (2006)
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)
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
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)
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)
T.S. Young, P.G. Schultz, Beyond the canonical 20 amino acids: expanding the genetic lexicon. J. Biol. Chem. 285, 11039–11044 (2010)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/978-3-319-54621-6_2
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-54620-9
Online ISBN: 978-3-319-54621-6
eBook Packages: Computer ScienceComputer Science (R0)