PromAn: An integrated knowledge-based web server dedicated to promoter analysis

Nucleic Acids Research

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

  Lardenois, Aurélie ^b   Chalmel, Frédéric ^a   Bianchetti, Laurent ^b   Sahel, José Alain ^c   Léveillard, Thierry ^c   Poch, Olivier ^b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^c INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; FUNCTIONAL GENOMICS; GENE SEQUENCE; HYPOTHESIS; KNOWLEDGE BASE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; SCORING SYSTEM; SEQUENCE ALIGNMENT; TRANSCRIPTION INITIATION SITE; VALIDATION PROCESS; BINDING SITE; GENETIC DATABASE; GENOMICS; INTERNET; METABOLISM; METHODOLOGY; SYSTEM ANALYSIS;

TRANSCRIPTION FACTOR;

BINDING SITES; DATABASES, GENETIC; GENOMICS; INTERNET; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; SOFTWARE; SYSTEMS INTEGRATION; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; USER-COMPUTER INTERFACE;

EID: 33747839771     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl193     Document Type: Article

References (21)

1. Sandelin,A., Wasserman,W.W. and Lenhard,B. (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res., 32, W249-W252.
2. Loots,G.G. and Ovcharenko,I. (2004) rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res., 32, W217-W221.
3. Tagle,D.A., Koop,B.F., Goodman,M., Slightom,J.L., Hess,D.L. and Jones,R.T. (1988) Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol., 203, 439-455.
4. Wasserman,W.W., Palumbo,M., Thompson,W., Fickett,J.W. and Lawrence,C.E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nature Genet., 26, 225-228.
5. Berezikov,E., Guryev,V. and Cuppen,E. (2005) CONREAL web server: identification and visualization of conserved transcription factor binding sites. Nucleic Acids Res., 33, W447-W450.
6. Corcoran,D.L., Feingold,E. and Benos,P.V. (2005) FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res., 33, W442-W446.
7. Yamashita,R., Suzuki,Y., Wakaguri,H., Tsuritani,K., Nakai,K. and Sugano,S. (2006) DBTSS: database of human transcription start sites, progress report 2006. Nucleic Acids Res., 34, D86-D89.
8. Schmid,C.D., Perier,R., Praz,V. and Bucher,P. (2006) EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res., 34, D82-D85.
9. Davuluri,R.V., Grosse,I. and Zhang,M.Q. (2001) Computational identification of promoters and first exons in the human genome. Nature Genet., 29, 412-417.
10. Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res., 12, 458-461.
11. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
12. Matys,V., Kel-Margoulis,O.V., Fricke,E., Liebich,I., Land,S., Barre-Dirrie,A., Reuter,I., Chekmenev,D., Krull,M., Hornischer,K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
13. Vlieghe,D., Sandelin,A., De Bleser,P.J., Vleminckx,K., Wasserman,W.W., van Roy,F. and Lenhard,B. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res., 34, D95-D97.
14. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
15. Lenhard,B., Sandelin,A., Mendoza,L., Engstrom,P., Jareborg,N. and Wasserman,W.W. (2003) Identification of conserved regulatory elements by comparative genome analysis. J. Biol., 2, 13.
16. Blanchette,M., Kent,W.J., Riemer,C., Elnitski,L., Smit,A.F., Roskin,K.M., Baertsch,R., Rosenbloom,K., Clawson,H., Green,E.D. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
17. Valdar,W.S. (2002) Scoring residue conservation. Proteins, 48, 227-241.
18. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
19. Mitton,K.P., Swain,P.K., Chen,S., Xu,S., Zack,D.J. and Swaroop,A. (2000) The leucine zipper of NRL interacts with the CRX homeodomain. A possible mechanism of transcriptional synergy in rhodopsin regulation. J. Biol. Chem., 275, 29794-29799.
20. Chen,S., Wang,Q.L., Nie,Z., Sun,H., Lennon,G., Copeland,N.G., Gilbert,D.J., Jenkins,N.A. and Zack,D.J. (1997) Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes. Neuron, 19, 1017-1030.
21. Brudno,M., Do,C.B., Cooper,G.M., Kim,M.F., Davydov,E., Green,E.D., Sidow,A. and Batzoglou,S. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13, 721-731.