Inferring combinatorial regulation of transcription in silico

Nucleic Acids Research

Volumn 33, Issue 1, 2005, Pages 272-279

  Blüthgen, Nils ^a   Kiełbasa, Szymon M ^a   Herzel, Hanspeter ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FACTOR; CELL DNA; LIPOPOLYSACCHARIDE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MEF; TRANSCRIPTION FACTOR MYF 2; TRANSCRIPTION FACTOR TEF; UNCLASSIFIED DRUG; MYOGENIC FACTOR;

ACCURACY; ANALYTIC METHOD; ARTICLE; BINDING SITE; COMBINATORIAL CHEMISTRY; COMPUTER MODEL; CONTROLLED STUDY; DNA FLANKING REGION; DNA MICROARRAY; FUNCTIONAL ASSESSMENT; GENE EXPRESSION; GENE INDUCTION; GENE SEQUENCE; GENE TARGETING; INTERMETHOD COMPARISON; MOLECULAR INTERACTION; NOMENCLATURE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; SKELETAL MUSCLE; STATISTICAL ANALYSIS; TRANSCRIPTION REGULATION; ALGORITHM; BIOLOGY; COMPUTER PROGRAM; EVALUATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HUMAN; METABOLISM; METHODOLOGY; TRANSACTIVATION;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; LIPOPOLYSACCHARIDES; MUSCLE, SKELETAL; MYOGENIC REGULATORY FACTORS; SOFTWARE; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS;

EID: 13744251104     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki167     Document Type: Article

References (23)

1. Cawley,S., Bekiranov,S., Ng,H.H., Kapranov,P., Sekinger,E.A., Kampa,D., Piccolboni,A., Sementchenko,V., Cheng,J., Williams,A.J. et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 116, 499-509.
2. Euskirchen,G., Royce,T.E., Bertone,P., Martone,R., Rinn,J.L., Nelson,F.K., Sayward,F., Luscombe,N.M., Miller,P., Gerstein,M., Weissman,S. and Snyder,M. (2004) CREB binds to multiple loci on human chromosome 22. Mol. Cell Biol., 24, 3804-3814.
3. Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nature Rev. Genet., 5, 276-287.
4. Pilpel,Y., Sudarsanam,P. and Church,G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet., 29, 153-159.
5. Kielbasa,S.M., Blüthgen,N., Sers,C., Schäfer,R. and Herzel,H. (2004) Prediction of cis-regulatory elements of coregulated genes. Genome Informatics, 15, 117-124.
6. 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.
7. Dieterich,C., Wang,H., Rateitschak,K., Luz,H. and Vingron,M. (2003) CORG: a database for comparative regulatory genomics. Nucleic Acids Res., 31, 55-57.
8. Frith,M.C., Li,M.C. and Weng,Z. (2003) Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31, 3666-3668.
9. 2/M checkpoints. Genes Dev., 16, 245-256.
10. Martone,R., Euskirchen,G., Bertone,P., Hartman,S., Royce,T.E., Luscombe,N.M., Rinn,J.L., Nelson,F.K., Miller,P., Gerstein,M., Weissman,S. and Snyder,M. (ZO03) Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA, 100, 12247-12252.
11. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
12. Blüthgen,N., Kielbasa,S.M., Cajavec,B. and Herzel,H. (2004) HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics, 20, 125-126.
13. Kielbasa,S.M., Blüthgen,N. and Herzel,H. (2004) Genome-wide analysis of functions regulated by sets of transcription factors. In Giegerich,R. and Stoye,J. (eds.), German Conference on Bioinformatics 2004. Gesellschaft für Informatik, Bonn Vol. P-5 3, pp. 105-113.
14. Wasserman,W.W. and Fickett,J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
15. Fessele,S., Boehlk,S., Mojaat, N., Miyamoto,N.G., Werner,T., Nelson,E.L., Schlondorff,D. and Nelson,P.J. (2001) Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells. FASEB J., 15, 577-579.
16. Birney,E., Andrews,D., Bevan,P., Caccamo,M., Cameron,G., Chen,Y., Clarke,L., Coates,G., Cox,T., Cuff,J. et al. (2004) Ensembl 2004. Nucleic Acids Res., 32, D468-D470.
17. Dieterich,C., Cusack,B., Wang,H., Rateitschak,K., Krause,A. and Vingron,M. (2002) Annotating regulatory DNA based on man-mouse genomic comparison. Bioinformatics, 18, S84-S90.
18. Fessele,S., Maier,H., Zischek,C., Nelson,P.J. and Werner,J. (2002) Regulatory context is a crucial part of gene function. Trends Genet., 18, 60-63.
19. Heinemeyer,T., Wingender,E., Reuter,I., Hermjakob,H., Kel,A.E., Kel,O.V., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Kolpakov,F.A., Podkolodny,N.L. and Kolchanov,N.A. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res., 26, 362-367.
20. Swanson,B.J., Jack,H.M. and Lyons,G.E. (1998) Characterization of myocyte enhancer factor 2 (MEF2) expression in B and T cells: MEF2C is a B cell-restricted transcription factor in lymphocytes. Mol. Immunol., 35, 445-458.
21. Werner,T., Fessele,S., Maier,H. and Nelson,P. (2003) Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J., 17, 1228-1237.
22. Gekakis,N., Staknis,D., Nguyen,H., Davis,F., Wilsbacher,L., King,D., Takahashi,J. and Weitz,C. (1998) Role of the clock protein in the mammalian circadian mechanism. Science, 280, 1564-1569.
23. Sandelin,A., Alkema,W., Engstrom,P., Wasserman,W.W. and Lenhard,B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32 D91-D94.