68
Views
4
CrossRef citations to date
0
Altmetric
Review

Improved understanding of gene expression regulation using systems biology

, &
Pages 915-924 | Published online: 09 Jan 2014

References

  • Anderson L, Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18, 533–537 (1997).
  • Griffin TJ, Gygi SP, Ideker T et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1(4), 323–333 (2002).
  • Lee PS, Shaw LB, Choe LH, Mehra A, Hatzimanikatis V, Lee KH. Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnol. Bioeng. 84(7), 834–841 (2003).
  • Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19(3), 1720–1730 (1999).
  • Ross PL, Huang YLN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154–1169 (2004).
  • Mehra A, Lee KH, Hatzimanikatis V. Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol. Bioeng. 84(7), 822–833 (2003).
  • Hatzimanikatis V, Lee KH. Dynamical analysis of gene networks requires both mRNA and protein expression information. Metab. Eng. 1(4), 275–281 (1999).
  • Wiener N. Cybernetics or Control and Communication in the Animal and the Machine. The MIT Press, Cambridge, UK (1948).
  • Mesarovic MD. System Theory and Biology. Springer-Verlag, NY, USA (1968).
  • Bertalanffy LV. General System Theory, Foundations, Development, Applications. George Braziller, NY, USA (1969).
  • Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343–372 (2001).
  • Kitano H. Systems biology: a brief overview. Science 295(5560), 1662–1664 (2002).
  • Aggarwal K, Lee KH. Functional genomics and proteomics as a foundation for systems biology. Brief Funct. Genomic Proteomic 2(3), 175–184 (2003).
  • Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature 405(6788), 827–836 (2000).
  • Selinger DW, Cheung KJ, Mei R et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol. 18(12), 1262–1268 (2000).
  • Fehlbaum P, Guihal C, Bracco L, Cochet O. A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. 33(5), e47 (2005).
  • Garcia CK, Mues G, Liao YL et al. Sequence diversity in genes of lipid metabolism. Genome Res. 11(6), 1043–1052 (2001).
  • Cho RJ, Mindrinos M, Richards DR et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet. 23(2), 203–207 (1999).
  • O’Farrell PH. High-resolution 2-dimensional electrophoresis of proteins. J. Biol. Chem. 250(10), 4007–4021 (1975).
  • Finehout EJ, Lee KH. An introduction to mass spectrometry applications in biological research. Biochem. Mol. Biol. Edu. 32(2), 93–100 (2004).
  • Lee KH. Proteomics: a technology-driven and technology-limited discovery science. Trends Biotechnol. 19(6), 217–222 (2001).
  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17(10), 994–999 (1999).
  • Cagney G, Emili A. De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nature Biotechnol. 20(2), 163–170 (2002).
  • Conrads TP, Alving K, Veenstra TD et al. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73(9), 2132–2139 (2001).
  • Yao XD, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73(13), 2836–2842 (2001).
  • Thompson A, Schafer J, Kuhn K et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75(8), 1895–1904 (2003).
  • Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L. Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23(1), 131–142 (2000).
  • von Roepenack-Lahaye E, Degenkolb T, Zerjeski M et al. Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol. 134(2), 548–559 (2004).
  • Fiehn O. Metabolomics – the link between genotypes and phenotypes. Plant Mol. Biol. 48(1–2), 155–171 (2002).
  • Grivet JP, Delort AM, Portais JC. NMR and microbiology: from physiology to metabolomics. Biochimie 85(9), 823–840 (2003).
  • Bartel PL, Roecklein JA, SenGupta D, Fields S. A protein linkage map of Escherichia coli bacteriophage T7. Nature Genet. 12(1), 72–77 (1996).
  • Ren B, Robert F, Wyrick JJ et al. Genome-wide location and function of DNA binding proteins. Science 290(5500), 2306–2309 (2000).
  • Krylov AS, Zasedateleva OA, Prokopenko DV, Rouviere-Yaniv J, Mirzabekov AD. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29(12), 2654–2660 (2001).
  • Houseman BT, Huh JH, Kron SJ, Mrksich M. Peptide chips for the quantitative evaluation of protein kinase activity. Nature Biotechnol. 20(3), 270–274 (2002).
  • MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science 289(5485), 1760–1763 (2000).
  • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2), 185–193 (2003).
  • Irizarry RA, Hobbs B, Collin F et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2), 249–264 (2003).
  • Pan W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18(4), 546–554 (2002).
  • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98(9), 5116–5121 (2001).
  • Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA 97(18), 10101–10106 (2000).
  • Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac. Symp. Biocomput. 455–466 (2000).
  • Raamsdonk LM, Teusink B, Broadhurst D et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnol. 19(1), 45–50 (2001).
  • Nicholson JK, Lindon JC, Holmes E. ‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29(11), 1181–1189 (1999).
  • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30(1), 207–210 (2002).
  • Gollub J, Ball CA, Binkley G et al. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 31(1), 94–96 (2003).
  • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30 (2000).
  • Keseler IM, Collado-Vides J, Gama-Castro S et al. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33, D334–D337 (2005).
  • Krieger CJ, Zhang PF, Mueller LA et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32, D438–D442 (2004).
  • Berman HM, Westbrook J, Feng Z et al. The Protein Data Bank. Nucleic Acids Res. 28(1), 235–242 (2000).
  • Bader GD, Betel D, Hogue CWV. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31(1), 248–250 (2003).
  • Kopka J, Schauer N, Krueger S et al. [email protected]: the Golm Metabolome Database. Bioinformatics 21(8), 1635–1638 (2005).
  • Brazma A, Hingamp P, Quackenbush J et al. Minimum Information About a Microarray Experiment (MIAME) – toward standards for microarray data. Nature Genet. 29(4), 365–371 (2001).
  • Taylor CF, Paton NW, Garwood KL et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnol. 21(3), 247–254 (2003).
  • Bino RJ, Hall RD, Fiehn O et al. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9(9), 418–425 (2004).
  • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9(1), 67–103 (2002).
  • Gardner TS, Faith JJ. Reverse-engineering transcription control networks. Physics Life Rev. 2, 65–88 (2005).
  • Barabasi AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nature Rev. Genet. 5(2), 101–113 (2004).
  • Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292(5518), 929–934 (2001).
  • Smolen P, Hardin PE, Lo BS, Baxter DA, Byrne JH. Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK. Biophys. J. 86(5), 2786–2802 (2004).
  • Stephanopoulos GN, Aristidou AA, Nielsen J. Metabolic Engineering. Academic Press, NY, USA, (1998).
  • Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature 420(6912), 190–193 (2002).
  • Arndt RA, MacGregor MH. Nucleon–nucleon phase shift analyses by chi-squared minimization. In: Nuclear Physics. Alder B, Fernbach S, Rotenberg M (Eds), Academic Press, NY, 253–296 (1966).
  • Bevington PR, Robinson DK. Data Reduction and Error Analysis for the Physical Sciences. Third Ed. McGraw Hill, NY, USA (2003).
  • Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical Recipes in C: The Art of Scientific Computing. Second Ed. Cambridge University Press, NY, USA (1992).
  • Tawarmalani M, Sahinidis NV. Global optimization of mixed-integer nonlinear programs: a theoretical and computational study. Math. Program. 99(3), 563–591 (2004).
  • Brown KS, Sethna JP. Statistical mechanical approaches to models with many poorly known parameters. Phys. Rev. E. 68(2–1), 021904/021901–021904/021909 (2003).
  • Brown KS, Hill CC, Calero GA, Lee KH, Sethna JP, Cerione RA. The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys. Biol. 1, 184–195 (2004).
  • Kuznetsov YA. Elements of applied bifurcation theory. In: Applied Mathematical Sciences. Antman SS, Marsden JE, Sirovich L (Eds), Springer-Verlag, NY, USA, 112, (2004).
  • Finney A, Hucka M. Systems biology markup language: level 2 and beyond. Biochem. Soc. T. 31(6), 1472–1473 (2003).
  • Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics 20(16), 2829–2831 (2004).
  • Sauro HM, Hucka M, Finney A et al. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. Omics 7(4), 355–372 (2003).
  • Lee PS, Lee KH. Engineering HlyA hypersecretion in Escherichia coli based on proteomic and microarray analyses. Biotechnol. Bioeng. 89(2), 195–205 (2005).
  • Shaw LB, Zia RK, Lee KH. Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 68(2 Pt 1), 021910 (2003).
  • Beer DG, Kardia SLR, Huang CC et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nature Med. 8(8), 816–824 (2002).
  • Chen GA, Gharib TG, Wang H et al. Protein profiles associated with survival in lung adenocarcinoma. Proc. Natl Acad. Sci. USA 100(23), 13537–13542 (2003).
  • Wu R, Lin L, Beer DG et al. Amplification and overexpression of the L-MYC proto-oncogene in ovarian carcinomas. Am. J. Pathol. 162(5), 1603–1610 (2003).
  • Christopher R, Dhiman A, Fox J et al. Data-driven computer simulation of human cancer cell. In: Applications of Bioinformatics in Cancer Detection. Umar A, Kapetanovic I, Khan J (Eds), New York Academy of Sciences, NY, USA, 132–153 (2004).
  • Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc. Natl Acad. Sci. USA 101(2), 641–646 (2004).
  • Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP. Network component analysis: reconstruction of regulatory signals in biological systems. Proc. Natl Acad. Sci. USA 100(26), 15522–15527 (2003).
  • Toh KL, Jones CR, He Y et al. An hPeR2 phosphorylation site mutation in familial advanced sleep phase syndrome. Science 291(5506), 1040–1043 (2001).
  • Stanewsky R. Genetic analysis of the circadian system in Drosophila melanogaster and mammals. J. Neurobiol. 54(1), 111–147 (2003).
  • Stelling J, Gilles ED, Doyle FJ III. Robustness properties of circadian clock architectures. Proc. Natl Acad. Sci. USA 101(36), 13210–13215 (2004).
  • Smolen P, Baxter DA, Byrne JH. Modeling circadian oscillations with interlocking positive and negative feedback loops. J. Neurosci. 21(17), 6644–6656 (2001).
  • McDonald MJ, Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107(5), 567–578 (2001).

Websites

  • National Center for Biotechnology Information www.ncbi.nih.gov (Viewed November 2005)
  • Swiss-Prot Protein Knowledgebase http://us.expasy.org/sprot (Viewed November 2005)
  • Database of Interacting Proteins http://dip.doe-mbi.ucla.edu (Viewed November 2005)
  • Bio-SPICE: Open Source Systems Biology www.biospice.org (Viewed November 2005)
  • Python Programming Language www.python.org (Viewed November 2005)
  • Perl Programming Language www.perl.com (Viewed November 2005)
  • Simplified Wrapper and Interface Generator (SWIG) www.swig.org (Viewed November 2005)
  • Fortran to Python Interface Generator http://cens.ioc.ee/projects/f2py2e (Viewed November 2005)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.