Skip to main content

Networks in Cell Biology

  • Chapter
  • 1980 Accesses

Abstract

Both natural and artificial systems can be understood as the interaction of a given set of elements. Interactions lead to global behavior often beyond the simple sum of the properties of each element. Interactions create most behaviors around us: A meeting between two people, file transfers among computers, predator-prey dynamics, cell responses, complex protein formation or DNA-protein binding. Erom these interactions large-scale systems emerge as a mesh of relations: Society, Internet, food webs, organisms, tissues or cells. Such organizations cannot be reduced to individual properties and a global view is required.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Albert, R. (2005). Scale-free networks in cell biology. J. Cell Sci., 118 (Pt 21):4947–57.

    Article  PubMed  CAS  Google Scholar 

  • Albert, R. and Barabasi, A. L. (2002). Statistical mechanics of complex networks. Rev. Modern Phys., 74:47–97.

    Article  Google Scholar 

  • Albert, R., Jeong, H., and Barabasi, A. L. (1999). Diameter of the world-wide web. Nature, 401:130–131.

    Article  CAS  Google Scholar 

  • Albert, R., Jeong, H., and Barabasi, A. L. (2000). Error and attack tolerance of complex networks. Nature, 406(6794):378–82.

    Article  PubMed  CAS  Google Scholar 

  • Amaral, L.A.N., Scala, A., Barthél’emy, M., and H.E., Standley (2000). Classes of small-world networks. Proc. Natl. Acad. Sci. USA, 97:11149–11152.

    Article  PubMed  CAS  Google Scholar 

  • Amoutzias, G. D., Robertson, D. L., Oliver, S. G., and Bornberg-Bauer, E. (2004). Convergent networks by single-gene duplications in higher eukaryotes. EMBO Rep., 5(3):274 9.

    Article  PubMed  CAS  Google Scholar 

  • Barabasi, A.L. and Oltvai, Z.N. (2004). Network biology: Understanding the cell’s functional organization. Nat. Rev. Genet., 5(2):101–13.

    Article  PubMed  CAS  Google Scholar 

  • Baron, M., Norman, D.G., and Campbell, I.D. (1991). Protein modules. Trends Biochem. Sci., 16(1):13–17.

    Article  PubMed  CAS  Google Scholar 

  • Branden, C. and Tooze, J. (1999). Introduction to Protein Structure. Garland Publishing, Inc., New York.

    Google Scholar 

  • Davidson, I. (2003). The genetics of tbp and tbp-related factors. Trends Biochem. Sci., 28(7):391–8.

    Article  PubMed  CAS  Google Scholar 

  • Dimova, D. K. and Dyson, N. J. (2005). The E2F transcriptional network: Old acquaintances with new faces. Oncogene, 24(17):2810–26.

    Article  PubMed  CAS  Google Scholar 

  • Dorogovtsev, S. N. and Mendes, J. F. F. (2003). Evolution of networks: from biological nets to the internet and WWW. Oxford University Press., Oxford.

    Google Scholar 

  • Erdös, P. and Rényi, A. (1960). On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci., 5:17–60.

    Google Scholar 

  • Fernández, P. and Solé, R. V. (2005). Graphs as models of large-scale biochemical organization. In Bonchev, D. and Rouvray, D. H., editors, Complexity in chemistry, biology and ecology. Springer, New York.

    Google Scholar 

  • Ferrer, R. and Solé, R.V. (2001). The small world of human language. Proc. Roy. Soc. Lond. B, 268:2261–2265.

    Article  Google Scholar 

  • Gangloff, Y. G., Romier, C., Thuault, S., Werten, S., and Davidson, I. (2001). The histone fold is a key structural motif of transcription factor tfiid. Trends Biochem. Sci., 26(4):250–7.

    Article  PubMed  CAS  Google Scholar 

  • Gavin, A. C., Bosche, M., and Krause, R. et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415(6868): 141–7.

    Article  PubMed  CAS  Google Scholar 

  • Gayther, S. A., Batley, S. J., and Linger, L. et al. (2000). Mutations truncating the EP300 acetylase in human cancers. Nat. Genet., 24(3):300–3.

    Article  PubMed  CAS  Google Scholar 

  • Giot, L., Bader, J. S., and Brouwer, C. et al. (2003). A protein interaction map of drosophila melanogaster. Science, 302(5651):1727–36.

    Article  PubMed  CAS  Google Scholar 

  • Guelzim, N., Bottani, S., Bourgine, P., and Kepes, F. (2002). Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet., 31(1):60–3.

    Article  PubMed  CAS  Google Scholar 

  • Han, J. D., Dupuy, D., Bertin, N., Cusick, M. E., and Vidal, M. (2005). Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol, 23(7):839–44.

    Article  PubMed  CAS  Google Scholar 

  • Hartl, M., Bader, A.G., and Bister, K. (2003). Molecular targets of the oncogenic transcription factor jun. Curr. Cancer Drug Targets, 3(1):41–55.

    Article  PubMed  CAS  Google Scholar 

  • 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. USA, 98(8):4569–74.

    Article  PubMed  CAS  Google Scholar 

  • Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. (2001). Lethality and centrality in protein networks. Nature, 411(6833):41–2.

    Article  PubMed  CAS  Google Scholar 

  • Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., and Barabasi, A. L. (2000). The large-scale organization of metabolic networks. Nature, 407(6804):651–4.

    Article  PubMed  CAS  Google Scholar 

  • Joyce, D., Albanese, C, Steer, J., Fu, M., Bouzahzah, B., and Pestell, R.G. (2001). Nf-κb and cell-cycle regulation: the cyclin connection. Cytokine Growth Factor Rev, 12(1):73–90.

    Article  PubMed  CAS  Google Scholar 

  • Koide, R., Kobayashi, S., Shimohata, T., Ikeuchi, T., Maruyama, M., Saito, M., Yamada, M., Takahashi, H., and Tsuji, S. (1999). A neurological disease caused by an expanded cag trinucleotide repeat in the tata-binding protein gene: a new polyglutamine disease? Hum. Mol. Genet, 8(11):2047–53.

    Article  PubMed  CAS  Google Scholar 

  • Laudet, V. (1997). Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor. J. Mol. Endocrinol, 19(3):207–26.

    Article  PubMed  CAS  Google Scholar 

  • Ledent, V., Paquet, O., and Vervoort, M. (2002). Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol., 3(6):RESEARCH0030.

    Google Scholar 

  • Lee, T.I., Rinaldi, N.J., and Robert, F. et al. (2002). Transcriptional regulatory networks in saccharomyces cerevisiae. Science, 298(5594):799–804.

    Article  PubMed  CAS  Google Scholar 

  • Lee, T.I. and Young, R.A. (1998). Regulation of gene expression by tbp-associated proteins. Genes Dev., 12(10):1398–408.

    PubMed  CAS  Google Scholar 

  • Levine, M. and Tjian, R. (2003). Transcription regulation and animal diversity. Nature, 424(6945):147–51.

    Article  PubMed  CAS  Google Scholar 

  • Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P. O., Han, J. D., Chesneau, A., Hao, T., Goldberg, D. S., Li, N., Martinez, M., Rual, J. F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L. V., Berriz, G. F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H. W., Elewa, A., Baumgartner, B., Rose, D. J., Yu, H., Bosak, S., Sequerra, R., Eraser, A., Mango, S. E., Saxton, W. M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K. C., Harper, J. W., Cusick, M. E., Roth, F. P., Hill, D. E., and Vidal, M. (2004). A map of the interactome network of the metazoan c. elegans. Science, 303(5657):540–3.

    Article  PubMed  CAS  Google Scholar 

  • Liu, H., Dibling, B., Spike, B., Dirlam, A., and Macleod, K. (2004). New roles for the rb tumor suppressor protein. Curr. Opin. Genet. Dev., 14(1):55–64.

    Article  PubMed  CAS  Google Scholar 

  • Ma’ayan, A., Jenkins, S.L., Neves, S., Hasseldine, A., Grace, E., Dubin-Thaler, B., Eungdamrong, N.J., Weng, G., Ram, P.T., Rice, J.J., Kershenbaum, A., Stolovitzky, G.A., Blitzer, R.D., and Iyengar, R. (2005). Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science, 309(5737):1078–83.

    Article  PubMed  CAS  Google Scholar 

  • Maslov, S. and Sneppen, K. (2002). Specificity and stability in topology of protein networks. Science, 296(5569):910–3.

    Article  PubMed  CAS  Google Scholar 

  • McCraith, S., Holtzman, T., Moss, B., and Fields, S. (2000). Genome-wide analysis of vaccinia virus protein-protein interactions. Proc. Natl. Acad. Sci. USA, 97(9):4879–84.

    Article  PubMed  CAS  Google Scholar 

  • Milgram, S. (1967). The small-world problem. Psychol. Today, 2:60–67.

    Google Scholar 

  • Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., and Alon, U. (2002). Network motifs: Simple building blocks of complex networks. Science, 298(5594):824–7.

    Article  PubMed  CAS  Google Scholar 

  • Morgenstern, B. and Atchley, W. R. (1999). Evolution of BHLH transcription factors: modular evolution by domain shuffling? Mol. Biol. Evol., 16(12):1654–63.

    PubMed  CAS  Google Scholar 

  • Newman, M. (2002a). Random graphs as models of networks. In Bornholdt, S. and Schuster, H.G., editors, Handbook of Graphs and Networks. Wiley-VHC, Weinheim.

    Google Scholar 

  • Newman, M. E. (2002b). Assortative mixing in networks. Phys. Rev. Lett., 89(20):208701.

    Article  PubMed  CAS  Google Scholar 

  • Okuno, M., Kojima, S., Matsushima-Nishiwaki, R., Tsurumi, H., Muto, Y., Friedman, S. L., and Moriwaki, H. (2004). Retinoids in cancer chemoprevention. Curr. Cancer Drug Targets, 4(3):285–98.

    Article  PubMed  CAS  Google Scholar 

  • Ouzounis, C. A. and Karp, P. D. (2000). Global properties of the metabolic map of escherichia coli. Genome Res., 10(4):568–76.

    Article  PubMed  CAS  Google Scholar 

  • Palla, G., Derenyi, I., Farkas, I., and Vicsek, T. (2005). Uncovering the over-lapping community structure of complex networks in nature and society. Nature, 435(7043):814–8.

    Article  PubMed  CAS  Google Scholar 

  • Pastor-Satorras, R., Smith, E., and Solé, R.V. (2003). Evolving protein interaction networks through gene duplication. J. Theor. Biol, 222(2):199–210.

    Article  PubMed  CAS  Google Scholar 

  • Pelengaris, S. and Khan, M. (2003). The many faces of c-myc. Arch. Biochem. Biophys., 416(2):129–36.

    Article  PubMed  CAS  Google Scholar 

  • Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R., McCartney, R.R., Schmidt, M.C., Rachidi, N., Lee, S.J., Mah, A.S., Meng, L., Stark, M.J., Stern, D.F., De Virgilio, C., Tyers, M., Andrews, B., Gerstein, M., Schweitzer, B., Predki, P.F., and Snyder, M. (2005). Global analysis of protein phosphorylation in yeast. Nature, 438(7068):679–84.

    Article  PubMed  CAS  Google Scholar 

  • Quong, M. W., Romanow, W. J., and Murre, C. (2002). E protein function in lymphocyte development. Annu. Rev. Immunol., 20:301–22.

    Article  PubMed  CAS  Google Scholar 

  • Radicchi, F., Castellano, C., Cecconi, F., Loreto, V., and Parisi, D. (2004). Defining and identifying communities in networks. Proc. Natl. Acad. Sci. USA, 101(9):2658–63.

    Article  PubMed  CAS  Google Scholar 

  • 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(6817):211–5.

    Article  PubMed  CAS  Google Scholar 

  • Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., and Barabasi, A.L. (2002). Hierarchical organization of modularity in metabolic networks. Science, 297(5586):1551–5.

    Article  PubMed  CAS  Google Scholar 

  • Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari, D., Sherman, B.K., and Yu, G. (2000). Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science, 290(5499):2105–10.

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez-Caso, C., Medina, M.A., and Solé, R.V. (2005). Topology, tinkering and evolution of the human transcription factor network. FEBS J. 272(24):6423–34.

    Article  PubMed  CAS  Google Scholar 

  • Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L. V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P., and Vidal, M. (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437(7062):1173–8.

    Article  PubMed  CAS  Google Scholar 

  • Salgado, H., Gama-Castro, S., Martinez-Antonio, A., Diaz-Peredo, E., Sanchez-Solano, F., Peralta-Gil, M., Garcia-Alonso, D., Jimenez-Jacinto, V., Santos-Zavaleta, A., Bonavides-Martinez, C., and Collado-Vides, J. (2004). RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res., 32 (Database issue):D303-6.

    Google Scholar 

  • Seidman, S. B. (1983). Network structure and minimum degree. Social Networks, 5:269–287.

    Article  Google Scholar 

  • Sharrocks, A.D. (2001). The ETS-domain transcription factor family. Nat. Rev. Mol. Cell Biol., 2(11):827–37.

    Article  PubMed  CAS  Google Scholar 

  • Shen-Orr, S.S., Milo, R., Mangan, S., and Alon, U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31(1):64–8.

    Article  PubMed  CAS  Google Scholar 

  • Solé, R.V. and Montoya, J.M. (2001). Complexity and fragility in ecological networks. Proc. Roy. Soc. Lond. B Biol. Sci., 268(1480):2039–45.

    Article  Google Scholar 

  • Solé, S.V. and Valverde, S. (2006). Are networks motifs the spandrels of cellular complexity? TREE, 21(8):419–422.

    PubMed  Google Scholar 

  • Sonnhammer, E.L. and Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci., 3(3):482–92.

    Article  PubMed  CAS  Google Scholar 

  • Stelzl, U., Worm, U., Lalowski, M., Haenig, C, Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., and Wanker, E.E. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122(6):957–68.

    Article  PubMed  CAS  Google Scholar 

  • Sunters, A., Thomas, D.P., Yeudall, W.A., and Grigoriadis, A.E. (2004). Accelerated cell cycle progression in osteoblasts overexpressing the c-fos protooncogene: induction of cyclin a and enhanced cdk2 activity. J. Biol. Chem. 279(11):9882–91.

    Article  PubMed  Google Scholar 

  • Tanaka, J. (2005). Scale-rich metabolic networks. Phys. Rev. Lett, 94:168101.

    Article  PubMed  CAS  Google Scholar 

  • Thiel, G., Lietz, M., and Hohl, M. (2004). How mammalian transcriptional repressors work. Eur. J. Biochem., 271(14):2855–62.

    Article  PubMed  CAS  Google Scholar 

  • 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(6770):623–7.

    Article  PubMed  CAS  Google Scholar 

  • Uetz, P. and Hughes, R. E. (2000). Systematic and large-scale two-hybrid screens. Curr. Opin. Microbiol, 3(3):303–8.

    Article  PubMed  CAS  Google Scholar 

  • Vázquez, A., Pastor-Satorras, R., and Vespignani, A. (2002). Large-scale topological and dynamical properties of the internet. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 65(6 Pt 2):066130.

    PubMed  Google Scholar 

  • Vousden, K. H. and Prives, C. (2005). P53 and prognosis: New insights and further complexity. Cell, 120(1):7–10.

    PubMed  CAS  Google Scholar 

  • Wagner, A. (2003). How the global structure of protein interaction networks evolves. Proc. Biol. Sci., 270(1514):457–66.

    Article  PubMed  CAS  Google Scholar 

  • Wagner, A. and Fell, D. A. (2001). The small world inside large metabolic networks. Proc. Biol. Sci., 268(1478):1803–10.

    Article  PubMed  CAS  Google Scholar 

  • Walhout, A.J., Boulton, S.J., and Vidal, M. (2000). Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast, 17(2):88–94.

    Article  PubMed  CAS  Google Scholar 

  • Watts, D. J. and Strogatz, S. H. (1998). Collective dynamics of’ small-world’ networks. Nature, 393(6684):440–2.

    Article  PubMed  CAS  Google Scholar 

  • 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(1):281–3.

    Article  PubMed  CAS  Google Scholar 

  • Wyrick, J.J. and Young, R.A. (2002). Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev., 12(2):130–6.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Rodríguez-Caso, C., Solé, R.V. (2007). Networks in Cell Biology. In: Dubitzky, W., Granzow, M., Berrar, D. (eds) Fundamentals of Data Mining in Genomics and Proteomics. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-47509-7_10

Download citation

Publish with us

Policies and ethics