Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Zhang, Shaoqiang ^a,b   Li, Shan ^a   Pham, Phuc T ^a   Su, Zhengchang ^a  

^a University of North Carolina at Charlotte   (United States)

^b TIANJIN NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; E. COLI; FIRMICUTES; PARAMETER SETTING; PREDICTION ACCURACY; PROKARYOTIC GENOMES; SUBTILIS; TRANSCRIPTION FACTOR BINDING SITES;

ALGORITHMS; ESCHERICHIA COLI; FORECASTING; TRANSCRIPTION FACTORS;

GENES;

BACILLUS SUBTILIS; CYANOBACTERIA; ESCHERICHIA COLI; FIRMICUTES; PROKARYOTA; PROTEOBACTERIA;

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BACTERIAL GENOME; BACTERIUM; BINDING SITE; CHEMISTRY; CHROMOSOME MAP; CLASSIFICATION; DNA SEQUENCE; ESCHERICHIA COLI; GENETIC ASSOCIATION; GENETICS; METABOLISM; PHYLOGENY;

ALGORITHMS; BACTERIA; BINDING SITES; CHROMOSOME MAPPING; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOME-WIDE ASSOCIATION STUDY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 77954782940     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-397     Document Type: Article

References (44)

1. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One 2007, 2(5):e484. 10.1371/journal.pone.0000484, 1871613, 17534434.
2. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24(3):133-141.
3. McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 2001, 29(3):774-782. 10.1093/nar/29.3.774, 30389, 11160901.
4. Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol 2003, 21(4):435-439. 10.1038/nbt802, 12627170.
5. van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc Natl Acad Sci USA 2002, 99(11):7323-7328. 10.1073/pnas.112690399, 124229, 12032281.
6. Alkema WB, Lenhard B, Wasserman WW. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res 2004, 14(7):1362-1373. 10.1101/gr.2242604, 442153, 15231752.
7. Jensen ST, Shen L, Liu JS. Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Bioinformatics 2005, 21(20):3832-3839. 10.1093/bioinformatics/bti628, 16105899.
8. Liu J, Xu X, Stormo GD. The cis-regulatory map of Shewanella genomes. Nucleic Acids Res 2008, 36(16):5376-5390. 10.1093/nar/gkn515, 2532739, 18701645.
9. Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res 2006, 34(7):1947-1958. 10.1093/nar/gkl138, 1435977, 16614445.
10. Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19(18):2369-2380. 10.1093/bioinformatics/btg329, 14668220.
11. Madan Babu M, Teichmann SA. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 2003, 31(4):1234-1244. 10.1093/nar/gkg210, 150228, 12582243.
12. Perez-Rueda E, Collado-Vides J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 2000, 28(8):1838-1847. 10.1093/nar/28.8.1838, 102813, 10734204.
13. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci USA 2000, 97(12):6652-6657. 10.1073/pnas.110147297, 18690, 10823905.
14. Moreno-Hagelsieb G, Collado-Vides J. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 2002, 18(Suppl 1):S329-336.
15. Wang T, Stormo GD. Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci USA 2005, 102(48):17400-17405. 10.1073/pnas.0505147102, 1297658, 16301543.
16. Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15(78):563-577. 10.1093/bioinformatics/15.7.563, 10487864.
17. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23(1):137-144. 10.1038/nbt1053, 15637633.
18. Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913. 10.1093/nar/gki791, 1199555, 16284194.
19. Zhang S, Xu M, Li S, Su Z. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res 2009, 37(10):e72. 10.1093/nar/gkp248, 2691844, 19383880.
20. Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2008, (36 Database):D120-124. 2238961, 18158297.
21. Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008, (36 Database):D93-96. 2247474, 17962296.
22. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
23. Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 127-138.
24. Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouze P, Moreau Y. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113-1122. 10.1093/bioinformatics/17.12.1113, 11751219.
25. Olman V, Xu D, Xu Y. CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol 2003, 1(1):21-40. 10.1142/S0219720003000162, 15290780.
26. Liu XS, Brutlag DL, Liu JS. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20(8):835-839.
27. Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Res 2006, (34 Web Server):W566-570. 10.1093/nar/gkl285, 1538899, 16845071.
28. Stormo GD, Hartzell GW. Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA 1989, 86(4):1183-1187. 10.1073/pnas.86.4.1183, 286650, 2919167.
29. Lozada-Chavez I, Janga SC, Collado-Vides J. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 2006, 34(12):3434-3445. 10.1093/nar/gkl423, 1524901, 16840530.
30. McCue LA, Thompson W, Carmack CS, Lawrence CE. Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res 2002, 12(10):1523-1532. 10.1101/gr.323602, 187528, 12368244.
31. van Dongen S. Graph clustering by flow simulation. PhD thesis 2000, University of Utrecht.
32. Mao F, Dam P, Chou J, Olman V, Xu Y. DOOR: a database for prokaryotic operons. Nucleic Acids Res 2009, (37 Database):D459-463. 10.1093/nar/gkn757, 2686520, 18988623.
33. Dam P, Olman V, Harris K, Su Z, Xu Y. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 2007, 35(1):288-298. 10.1093/nar/gkl1018, 1802555, 17170009.
34. Moreno-Campuzano S, Janga SC, Perez-Rueda E. Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach. BMC Genomics 2006, 7:147. 10.1186/1471-2164-7-147, 1524751, 16772031.
35. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA. DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 2008, (36 Database):D88-92. 2238844, 18073188.
36. Kummerfeld SK, Teichmann SA. DBD: a transcription factor prediction database. Nucleic Acids Res 2006, (34 Database):D74-81. 10.1093/nar/gkj131, 1347493, 16381970.
37. Suzuki S, Ferjani A, Suzuki I, Murata N. The SphS-SphR two component system is the exclusive sensor for the induction of gene expression in response to phosphate limitation in synechocystis. J Biol Chem 2004, 279:13234-13240. 10.1074/jbc.M313358200, 14707128.
38. Su Z, Olman V, Xu Y. Computational prediction of Pho regulons in cyanobacteria. BMC Genomics 2007, 8:156. 10.1186/1471-2164-8-156, 1906773, 17559671.
39. Su Z, Olman V, Mao F, Xu Y. Comparative genomics analysis of ntcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acid Res 2005, 33(16):5156-5171. 10.1093/nar/gki817, 1214546, 16157864.
40. Herrero A, Muro-Pastor AM, Valladares A, Flores E. Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria. FEMS Microbiol Rev 2004, 28(4):469-487. 10.1016/j.femsre.2004.04.003, 15374662.
41. Xu M, Su Z. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes. BMC Genomics 2009, 10:23. 10.1186/1471-2164-10-23, 2633013, 19146659.
42. Bollet C, Grimont P, Gainnier M, Geissler A, Sainty JM, De Micco P. Fatal pneumonia due to Serratia proteamaculans subsp. quinovora. J Clin Microbiol 1993, 31(2):444-445. 262785, 8432835.
43. Brouwer RW, Kuipers OP, van Hijum SA. The relative value of operon predictions. Brief Bioinform 2008, 9(5):367-375. 10.1093/bib/bbn019, 18420711.
44. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 1996, 93:10268-10273.