The relative value of operon predictions

Briefings in Bioinformatics

Volumn 9, Issue 5, 2008, Pages 367-375

  Brouwer, Rutger W W ^a   Kuipers, Oscar P ^a   Van Hijum, Sacha A F T ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Bioinformatics; Computational prediction; Operon

Indexed keywords

SPACER DNA; TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; BACILLUS SUBTILIS; BIOINFORMATICS; COMPUTER PREDICTION; DNA MICROARRAY; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; GENE CLUSTER; GENE EXPRESSION PROFILING; GENETIC CONSERVATION; NONHUMAN; OPEN READING FRAME; OPERON; SEQUENCE DATABASE; TRANSCRIPTOMICS;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTER SIMULATION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OPERON; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

BACILLUS SUBTILIS; ESCHERICHIA COLI;

EID: 50049106504     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn019     Document Type: Article

References (53)

1. Wolf YI, Rogozin IB, Kondrashov AS, et al. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 2001;11:356-72.
2. Okuda S, Katayama T, Kawashima S, et al. ODB: A database of operons accumulating known operons across multiple genomes. Nucleic Acids Res 2006;34:D358-62.
3. Okuda S, Kawashima S, Kobayashi K, et al. Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 2007;8 48.
4. Price MN, Arkin AP, Alm EJ. The life-cycle of operons. PLoS Genet 2006;2:e96.
5. Price MN, Huang KH, Arkin AP, et al. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 2005;15:809-19.
6. Lawrence JG, Roth JR. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 1996;143: 1843-60.
7. Zheng Y, Szustakowski JD, Fortnow L, et al. Computational identification of operons in microbial genomes. Genome Res 2002; 12:1221-30.
8. Romero PR, Karp PD. Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics 2004;20:709-17.
9. Siefert JL, Martin KA, Abdi F, et al. Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA. J Mol Evol 1997;45:467-72.
10. Ermolaeva MD, White O, Salzberg SL. Prediction of operons in microbial genomes. Nucleic Acids Res 2001;29: 1216-21.
11. Overbeek R, Fonstein M, D'Souza M, et al. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 1999;96 2896-901.
12. Yan B, Methe BA, Lovley DR, et al. Computational prediction of conserved operons and phylogenetic foot-printing of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae. J Theor Biol 2004; 230:133-44.
13. Price MN, Arkin AP, Alm EJ. OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics 2006;7:19.
14. Carpentier AS, Riva A, Tisseur P, et al. The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA. Comput Biol Chem 2004;28 3-10.
15. Salgado H, Gama-Castro S, Peralta-Gil M, et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res 2006;34:D394-97.
16. Itoh T, Takemoto K, Mori H, et al. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol 1999;16:332-46.
17. Sierro N, Makita Y, de Hoon M, et al. DBTBS: A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008;36:D93-6.
18. Yada T, Nakao M, Totoki Y, et al. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics 1999;15:987-93.
19. Craven M, Page D, Shavlik J, et al. A probabilistic learning approach to whole-genome operon prediction. Proc Int Conf Intell Syst Mot Biol 2000;8:116-27.
20. Salgado H. Morrno-Hagelsieb G. Smith TF, et al. Operons in Escherichia coli: Genomic analyses and predictions. Proc Natl Acad Sci USA 2000;97:6652-7.
21. Moreno-Hagelsieb G, Collado-Vides J. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 2002; 18:S329-36.
22. Moreno-Hagelsieb G, Collado-Vides J. Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context. In Silico Biol 2002;2:87-95.
23. Sabatti C, Rohlin L, Oh MK, et al. Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res 2002;30:2886-93.
24. Tjaden B, Saxena RM, Stolyar S, et al. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 2002;30:3732-8.
25. Bockhorst J, Qiu Y, Glasner J, et al. Predicting bacterial transcription units using sequence and expression data. Bioinformatics 2003;19(Suppl. 1):i34-43.
26. Bockhorst J, Craven M, Page D, et al. A Bayesian network approach to operon prediction. Bioinformatics 2003;19:1227-35.
27. Chen X, Su Z, Xu Y, et al. Computational prediction of operons in Synechococcus sp. WH8102. Genome Inform 2004; 15 211-22.
28. Chen X, Su Z, Dam P, et al. Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res 2004;32:2147-57.
29. De Hoon MJ, Imoto S, Kobayashi K, et al. Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac Symp Biocomput 2004;276-87.
30. Paredes CJ, Rigoutsos I, Papoutsakis ET. Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res 2004;32:1973-81.
31. Steinhauser D, Junker BH, Luedemann A, et al. Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics 2004;20:1928-39.
32. Wang L, Trawick JD, Yamamoto R, et al. Genome-wide operon prediction in Staphylococcus aureus. Nucleic Acids Res 2004;32 3689-702.
33. De Hoon MJ, Makita Y, Nakai K, et al. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol 2005;1:e25.
34. Edwards MT, Rison SCG, Stoker NG, et al. A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. Nucleic Acids Res 2005;33:3253-62.
35. Jacob E, Sasikumar R, Nair KN. A fuzzy guided genetic algorithm for operon prediction. Bioinformatics 2005;21: 1403-7.
36. Price MN, Huang KH, Alm EJ, et al. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 2005;33:880-92.
37. Westover BP, Buhler JD, Sonnenburg JL, et al. Operon prediction without a training set. Bioinformatics 2005;21: 880-8.
38. Janga SC, Lamboy WF, Huerta AM, et al. The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucleic Acids Res 2006;34: 3980-7.
39. Zhang GQ, Cao ZW, Luo QM, et al. Operon prediction based on SVM. Comput Biol Chem 2006;30:233-40.
40. Bergman NH, Passalacqua KD, Hanna PC, et al. Operon Prediction for sequenced bacterial genomes without experimental information. Appl Environ Microbiol 2007;73: 846-54.
41. Charaniya S, Mehra S, Lian W, et al. Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor. Nucleic Acids Res 2007;35:7222-36.
42. Dam P, Olman V, Harris K, et al. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 2007;35:288-98.
43. Roback P, Beard J, Baumann D, et al. A predicted operon map for Mycobacterium tuberculosis. Nucleic Acids Res 2007;35: 5085-95.
44. Tran TT, Dam P, Su Z, et al. Operon prediction in Pyrococcus furiosus. Nucleic Acids Res 2007;35:11-20.
45. Laing E, Sidhu K, Hubbard SJ. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics 2008;9:79.
46. Riley M. Functions of the gene products of Escherichia coli. Microbiol Mol Biol Rev 1993;57:862-952.
47. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631-7.
48. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
49. Ermolaeva MD, Khalak HG, White O, et al. Prediction of transcription terminators in bacterial genomes. J Mol Biol 2000; 301:27-33.
50. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007;8:R22.
51. Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: Mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res 2007;35:D760-5.
52. Parkinson H, Kapushesky M, Shojatalab M, et al. Array Express - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007;35: D747-50.
53. Demeter J, Beauheim C, Gollub J, et al. The Stanford Microarray Database: Implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007; 35:D766-70.