Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  König, Rainer ^a,b   Schramm, Gunnar ^b   Oswald, Marcus ^a   Seitz, Hanna ^a   Sager, Sebastian ^a   Zapatka, Marc ^b   Reinelt, Gerhard ^a   Eils, Ronald ^a,b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC AND ANAEROBIC CONDITIONS; AMOUNT OF INFORMATION; ANAEROBIC CONDITIONS; BIOLOGICAL INTERACTIONS; ENVIRONMENTAL CONDITIONS; FEATURE EXTRACTION METHODS; MACHINE LEARNING METHODS; MICROARRAY TECHNOLOGIES;

BACTERIA; BIOCHEMISTRY; COMPLEX NETWORKS; ESCHERICHIA COLI; FEATURE EXTRACTION; GENE EXPRESSION; IODINE; LEARNING SYSTEMS; METABOLISM;

MATRIX ALGEBRA;

ASPARTIC ACID; FORMIC ACID; NICOTINAMIDE ADENINE DINUCLEOTIDE; ESCHERICHIA COLI PROTEIN; OXYGEN;

AEROBIC METABOLISM; AMINO ACID METABOLISM; ANAEROBIC METABOLISM; ARTICLE; BACTERIAL METABOLISM; CLASSIFICATION; CONTROLLED STUDY; ENZYME MECHANISM; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; FERMENTATION; GENE CLUSTER; GENE EXPRESSION; GENE INTERACTION; GENE MAPPING; GENETIC ASSOCIATION; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE METABOLISM; PATTERN RECOGNITION; ALGORITHM; ANAEROBIC GROWTH; BIOLOGICAL MODEL; COMPUTER SIMULATION; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; PROCEDURES; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

ALGORITHMS; ANAEROBIOSIS; COMPUTER SIMULATION; ENERGY METABOLISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, BIOLOGICAL; OXYGEN; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION;

EID: 33645792897     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-119     Document Type: Article

References (37)

1. Berg JM, Tymoczko, JL, Stryer L: Biochemistry. Fifth Edition edition. New York, W. H. Freeman; 2002:1050.
2. Karp PD, Riley M, Paley SM, Pellegrini-Toole A: The MetaCyc Database. Nucleic Acids Res 2002, 30:59-61.
3. Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C: DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci U S A 2000, 97:12170-12175.
4. Neidhardt FC: Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington D.C., American Society for Microbiology; 1996.
5. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
6. Stephanopoulos G, Hwang D, Schmitt WA, Misra J: Mapping physiological states from microarray expression measurements. Bioinformatics 2002, 18:1054-1063.
7. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257.
8. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
9. Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301:102-105.
10. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, 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, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
11. Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18 Suppl 1:S233-40.
12. Hanisch D, Zien A, Zimmer R, Lengauer T: Co-clustering of biological networks and gene expression data. Bioinformatics 2002, 18 Suppl 1:S145-54.
13. Zien A, Kuffner R, Zimmer R, Lengauer T: Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol 2000, 8:407-417.
14. König R, Eils R: Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics 2004, 20:1500-1505.
15. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96.
16. Tusher VG, Tibshirani R, Chu G: Significance analysis of micro-arrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98:5116-5121.
17. Ruschhaupt M, Huber W, Poustka A, Mansmann U: A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks. Stat Appl Genetics Mol Biol 2004, 3:37.
18. Bonferroni CE: Il calcolo delle assicurazioni su gruppi di test. In Studi in Onore del Professore Salvatore Ortu Carboni Rome, Italy, 1935:13-60.
19. Anderson JJ, Oxender DL: Genetic separation of high- and low-affinity transport systems for branched-chain amino acids in Escherichia coli K-12. J Bacteriol 1978, 136:168-174.
20. Ohnishi K, Hasegawa A, Matsubara K, Date T, Okada T, Kiritani K: Cloning and nucleotide sequence of the brnQ gene, the structural gene for a membrane-associated component of the LIV-II transport system for branched-chain amino acids in Salmonella typhimurium. Jpn J Genet 1988, 63:343-357.
21. Stephanopoulos G, Alper H, Moxley J: Exploiting biological complexity for strain improvement through systems biology. Nat Biotechnol 2004, 22:1261-1267.
22. Nelson SW, Binkowski DJ, Honzatko RB, Fromm HJ: Mechanism of action of Escherichia coli phosphoribosylaminoimidazole-succinocarboxamide synthetase. Biochemistry 2005, 44:766-774.
23. Wiame E, Van Schaftingen E: Fructoselysine 3-epimerase, an enzyme involved in the metabolism of the unusual Amadori compound psicoselysine in Escherichia coli. Biochem J 2004, 378:1047-1052.
24. Zyzak DV, Richardson JM, Thorpe SR, Baynes JW: Formation of reactive intermediates from Amadori compounds under physiological conditions. Arch Biochem Biophys 1995, 316:547-554.
25. Ollagnier-de Choudens S, Loiseau L, Sanakis Y, Barras F, Fontecave M: Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis. FEBS Lett 2005, 579:3737-3743.
26. Christof T, Oswald M, Reinelt G: Consecutive Ones and A Betweenness Problem in Computational Biology:. 6th IPCO Conference; Houston, Texas; 1998:213-228.
27. Tucker A: A Structure Theorem for the Consecutive I's Property. Journal of Combinatorial Theory B 1972, 12:153-162.
28. Booth KS, Lueker GS: Test for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms. J Comput Systems Sci 1976, 13:335-379.
29. Oswald M, Reinelt G: Polyhedral Aspects of the Consecutive Ones Problem: 5th Conference on Computing and Combinatorics; Sydney; 2000:373-382.
30. Alizadeh F, Karp RM, Weisser DK, Zweig G: Physical mapping of chromosomes using unique probes. ACM Press; 1994:489-500.
31. Greenberg DS, Istrail S: Physical mapping by STS hybridization: algorithmic strategies and the challenge of software evaluation. J Comput Biol 1995, 2:219-273.
32. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The large-scale organization of metabolic networks. Nature 2000, 407:651-654.
33. Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 2005, 33:D334-7.
34. Glasner JD, Liss P, Plunkett G, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT: ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 2003, 31:147-151.
35. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18 Suppl 1:S96-104.
36. Datsenko KA, Wanner BL: One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 2000, 97:6640-6645.
37. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia call K-12. Science 1997, 277:1453-1474.