iCR: A web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Ranjan, Sarita ^a   Seshadri, Jayshree ^a   Vindal, Vaibhav ^a   Yellaboina, Sailu ^a   Ranjan, Akash ^a  

^a CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN; BACTERIAL PROTEIN; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CLASSIFICATION; COMPUTER PROGRAM; GENE CONTROL; GENOME; INTERNET; ORTHOLOGY; PRIORITY JOURNAL; PROKARYOTE; REGULON; SEQUENCE ALIGNMENT; BACTERIAL GENOME; COMPUTER INTERFACE; GENOMICS; METABOLISM; METHODOLOGY; OPERON; REGULATORY SEQUENCE;

PROKARYOTA;

BACTERIAL PROTEINS; BINDING SITES; DNA-BINDING PROTEINS; GENOME, BACTERIAL; GENOMICS; INTERNET; OPERON; REGULATORY ELEMENTS, TRANSCRIPTIONAL; REGULON; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 33747816484     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl202     Document Type: Article

References (25)

1. Xing,B. and van der Laan,M.J. (2005) A causal inference approach for constructing transcriptional regulatory networks. Bioinformatics, 21, 4007-4013.
2. Hershberg,R., Yeger-Lotem,E. and Margalit,H. (2005) Chromosomal organization is shaped by the transcription regulatory network. Trends Genet. 21, 138-142.
3. Balazsi,G., Barabasi,A.L. and Oltvai,Z.N. (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl Acad. Sci. USA, 102, 7841-7846.
4. Ren,J. and Prescott,J.F. (2003) Analysis of virulence plasmid gene expression of intra-macrophage and in vitro grown Rhodococcus equi ATCC 33701. Vet. Microbiol., 94, 167-182.
5. Rodriguez,G.M., Voskuil,M.I., Gold,B., Schoolnik,G.K. and Smith,I. (2002) ideR, an essential gene in Mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun., 70, 3371-3381.
6. Lin,L.H., Lee,H.C., Li,W.H. and Chen,B.S. (2005) Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinformatics, 6, 258.
7. Wang,T. and Stormo,G.D. (2005) Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc. Natl Acad. Sci. USA, 102, 17400-17405.
8. Liu,X., Brutlag,D.L. and Liu,J.S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 127-138.
9. Liu,Y., Wei,L., Batzoglou,S., Brutlag,D.L., Liu,J.S. and Liu,X.S. (2004) A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res., 32, W204-W207.
10. Liu,Y., Liu,X.S., Wei,L., Altman,R.B. and Batzoglou,S. (2004) Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res., 14, 451-458.
11. Liu,X.S., Brutlag,D.L. and Liu,J.S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
12. Conlon,E.M., Liu,X.S., Lieb,J.D. and Liu,J.S. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
13. Jensen,S.T. and Liu,J.S. (2004) BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics, 20, 1557-1564.
14. Sinha,S., Blanchette,M. and Tompa,M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5, 170.
15. Yellaboina,S., Seshadri,J., Kumar,M.S. and Ranjan,A. (2004) PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. Nucleic Acids Res., 32, W318-W320.
16. Yellaboina,S., Ranjan,S., Chakhaiyar,P., Hasnain,S.E. and Ranjan,A. (2004) Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae. BMC Microbiol., 4, 38.
17. Prakash,P., Yellaboina,S., Ranjan,A. and Hasnain,S.E. (2005) Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames. Bioinformatics, 21, 2161-2166.
18. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C. and Collado-Vides,J. (2001) RegulonDB (Version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res., 29, 72-74.
19. Munch,R., Hiller,K., Barg,H., Heldt,D., Linz,S., Wingender,E. and Jahn,D. (2003) PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res., 31, 266-269.
20. Ishii,T., Yoshida,K., Terai,G., Fujita,Y. and Nakai,K. (2001) DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res., 29, 278-280.
21. Tatusov,R.L., Galperin,M.Y., Natale,D.A. and Koonin,E.V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
22. Tatusov,R.L., Natale,D.A., Garkavtsev, IV, Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
23. Little,J.W., Mount,D.W. and Yanisch-Perron,C.R. (1981) Purified lexA protein is a repressor of the recA and lexA genes. Proc. Natl Acad. Sci. USA, 78, 4199-4203.
24. Groban,E.S., Johnson,M.B., Banky,P., Burnett,P.G., Calderon,G.L., Dwyer,E.C., Fuller,S.N., Gebre,B., King,L.M., Sheren,I.N. et al. (2005) Binding of the Bacillus subtilis LexA protein to the SOS operator. Nucleic Acids Res., 33, 6287-6295.
25. Campoy,S., Salvador,N., Cortes,P., Erill,I. and Barbe,J. (2005) Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus. J. Bacteriol., 187, 5367-5375.