An approach to identify over-represented cis-elements in related sequences

Nucleic Acids Research

Volumn 31, Issue 7, 2003, Pages 1995-2005

  Zheng, Jiashun ^a   Wu, Jiajin ^a   Sun, Zhirong ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

ALGORITHM; ANALYTIC METHOD; AUTOMATION; BINDING SITE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE IDENTIFICATION; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; REVIEW; SCORING SYSTEM; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

ACTINS; ANIMALS; BINDING SITES; DNA; HEMOGLOBINS; HUMANS; INTERFERONS; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 0037386472     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg287     Document Type: Review

References (28)

1. Fickett,J.W. and Wasserman,W.W. (2000) Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol., 11, 19-24.
2. Halfon,M.S., Grad,Y., Church,G.M. and Michelson,A.M. (2002) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res., 12, 1019-1028.
3. Stormo,G.D. and Fields,D.S. (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci., 23, 109-113.
4. Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., Pruss,M., Reuter,I. and Schacherer,F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
5. Kolchanov,N.A., Podkolodnaya,O.A., Ananko,E.A., Ignatieva,E.V., Stepanenko,I.L., Kel-Margoulis,O.V., Kel,A.E., Merkulova,T.I., Goryachkovskaya,T.N., Busygina,T.V., Kolpakov,F.A., Podkolodny,N.L., Naumochkin,A.N., Korostishevskaya,I.M., Romashchenko,A.G. and Overton,G.C. (2000) Transcription regulatory regions database (TRRD): its status in 2000. Nucleic Acids Res., 28, 298-301.
6. Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
7. Kel,A.E., Kel-Margoulis,O.V., Farnham,P.J., Bartley,S.M., Wingender,E., and Zhang,M.Q. (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. J. Mol. Biol., 309, 99-120.
8. Ohler,U. and Niemann,H. (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet., 17, 56-60.
9. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
10. Bailey,T.L. and Elkan,C.P. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Altman,R., Brutlag,D., Karp,P., Lathrop,R. and Searls,D. (eds), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, USA, pp. 28-36.
11. GuhaThakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
12. van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
13. Praz,V., Perier,R., Bonnard,C. and Bucher,P. (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res., 30, 322-324.
14. Pickert,L., Reuter,I., Klawonn,F. and Wingender,E. (1998) Transcription regulatory region analysis using signal detection and fuzzy clustering. Bioinformatics, 14, 244-251.
15. Ma,H, Yanofsky,M.F. and Meyerowitz,E.M. (1991) AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Dev., 5, 484-495.
16. Frech,K., Quandt,K. and Werner,T. (1998) Muscle actin genes: a first step towards computational classification of tissue specific promoters. In Silico Biol., 1, 29-38.
17. Biesiada,E., Hamamori,Y., Kedes,L. and Sartorelli,V. (1999) Myogenic basic helix-loop-helix proteins and Sp1 interact as components of a multiprotein transcriptional complex required for activity of the human cardiac alpha-actin promoter. Mol. Cell. Biol., 19, 2577-2584.
18. Parakati,R. and DiMario,J.X. (2002) Sp1- and Sp3-mediated transcriptional regulation of the fibroblast growth factor receptor 1 gene in chicken skeletal muscle cells. J. Biol. Chem., 277, 9278-9285.
19. Sieweke,M.H. and Graf,T. (1998) A transcription factor party during blood cell differentiation. Curr. Opin. Genet. Dev., 8, 545-551.
20. Horak,C.E., Mahajan,M.C., Luscombe,N.M., Gerstein,M., Weissman,S.M. and Snyder,M. (2002) GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc. Natl Acad. Sci. USA, 99, 2924-2929.
21. Ryan,T.M., Sun,C.W., Ren,J. and Townes,T.M. (2000) Human gamma-globin gene promoter element regulates human beta-globin gene developmental specificity. Nucleic Acids Res., 28, 2736-2740.
22. Xu,X.S., Glazer,P.M. and Wang,G. (2000) Activation of human gamma-globin gene expression via triplex-forming oligonucleotide (TFO)-directed mutations in the gamma-globin gene 5′ flanking region. Gene, 242, 219-228.
23. Tada,Y., Ho,A., Matsuyama,T. and Mak,T.W. (1997) Reduced incidence and severity of antigen-induced autoimmune diseases in mice lacking interferon regulatory factor-1. J. Exp. Med., 185, 231-238.
24. Van Der Fits,L., Van Der Wel,L.I., Laman,J.D., Prens,E.P. and Verschuren,M.C. (2003) Psoriatic lesional skin exhibits an aberrant expression pattern of interferon regulatory factor-2 (IRF-2). J. Pathol., 199, 107-114.
25. Melen,K., Keskinen,P., Lehtonen,A. and Julkunen,I. (2000) Interferon-induced gene expression and signaling in human hepatoma cell lines. J. Hepatol., 33, 764-772.
26. Penix,L.A., Sweetser,M.T., Weaver,W.M., Hoeffler,J.P., Kerppola,T.K. and Wilson,C.B. (1996) The proximal regulatory element of the interferon-gamma promoter mediates selective expression in T cells. J. Biol. Chem., 271, 31964-31972.
27. Zhang,T. and Zhang,M. (2001) Promoter extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics, 17, 1232-1233.
28. Jakt,L.M., Cao,L., Cheah,K.S. and Smith,D.K. (2001) Assessing clusters and motifs from gene expression data. Genome Res., 11, 112-123.