MatInspector and beyond: Promoter analysis based on transcription factor binding sites

Bioinformatics

Volumn 21, Issue 13, 2005, Pages 2933-2942

  Cartharius, K ^a   Frech, K ^a   Grote, K ^a   Klocke, B ^a   Haltmeier, M ^a   Klingenhoff, A ^a   Frisch, M ^a   Bayerlein, M ^a   Werner, T ^a  

^a Genomatix GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COLLAGENASE 3; GALECTIN; NUCLEOTIDE; OSTEOCLAST DIFFERENTIATION FACTOR; TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPARATIVE STUDY; COMPUTER PROGRAM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING;

EID: 21444443478     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti473     Document Type: Article

References (48)

1. Alvarez,M. et al. (1997) Rat osteoblast and osteosarcoma nuclear matrix proteins bind with sequence specificity to the rat type I collagen promoter. Endocrinology, 138, 482-489.
2. Barash,Y. et al. (2004) CIS: compound importance sampling method for protein-DNA binding site P-value estimation. Bioinformatics, 5, 596-600.
3. Baum,K. et al. (1997) Improved ballistic transient transformation conditions for tomato fruit allow identification of organ-specific contributions of I-box and G-box to the RBCS2 promoter activity. Plant J., 12, 463-469.
4. Berezikov,E. et al. (2004) CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res., 14, 170-178.
5. Boehlk,S. et al. (2000) ATF and Jun transcription factors, acting through an Ets/CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cells. Eur J. Immunol., 30, 1102-1112.
6. Bucher,P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
7. Chen,Q.K. et al. (1995) MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci., 11, 563-566.
8. D'Alonzo,R.C. et al. (2002) Physical interaction of the activator protein-1 factors c-Fos and c-Jun with Cbfa1 for collagenase-3 promoter activation. J. Biol. Chem., 277, 816-822.
9. Dhamija,S. and Krebsbach,P.H. (2001) Role of Cbfa1 in ameloblastin gene transcription. J. Biol. Chem., 276, 35159-35164.
10. Doan,L.L. et al. (2004) Targeted transcriptional repression of Gfi1 by GFI1 and GFI1B in lympboid cells. Nucleic Acids Res., 32, 2508-2519.
11. Dyer,K.D. and Rosenberg,H.F. (2001) Transcriptional regulation of galectin-10 (eosinophil Charcot-Leyden crystal protein): a GC box (-44 to -50) controls butyric acid induction of gene expression. Life Sci., 69, 201-212.
12. Elkon,R. et al. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
13. Ellrott,K. et al. (2002) Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics, 18(Suppl 2), S100-S109.
14. Fessele,S. et al. (2002) Regulatory context is a crucial part of gene function. Trends Genet., 18, 60-63.
15. Garvie,C.W. and Wolberger,C. (2001) Recognition of specific DNA sequences. Mol. Cell, 8, 937-946.
16. Johnson,D.R. and Pober,J.S. (1994) HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons. Mol. Cell. Biol., 14, 1322-1332.
17. Kel,A.E. et al. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
18. Klingenhoff,A. et al. (1999) Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics, 15, 180-186.
19. Kodadek,T. (1998) Mechanistic parallels between DNA replication, recombination and transcription. Trends Biochem. Sci., 23, 79-83.
20. Kohonen,T. (1995) Self Organizing Maps. Springer Verlag, Heidelberg.
21. Lander,E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
22. Locker,J. et al. (2002) Definition and prediction of the full range of transcription factor binding sites-the hepatocyte nuclear factor 1 dimeric site. Nucleic Acids Res., 30, 3809-3817.
23. Loots,G.G. and Ovcharenko,I. (2004) rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res., 32, W217-W221.
24. Martinez-Hernandez,A. et al. (2002) Functional properties and regulatory complexity of a minimal RBCS light-responsive unit activated by phytochrome, cryptochrome, and plastid signals. Plant Physiol., 128, 1223-1233.
25. Matys,V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
26. Mengshol,J.A. et al. (2001) IL-1 induces collagenase-3 (MMP-13) promoter activity in stably transfected chondrocytic cells: requirement for Runx-2 and activation by p38 MAPK and JNK pathways. Nucleic Acids Res., 29, 4391-4372.
27. Morgenstern,B. et al. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294.
28. O'Brien,C.A. et al. (2002) Cbfa1 does not regulate RANKL gene activity in stromal/osteoblastic cells. Bone, 30, 453-462.
29. Ota,T. et al. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet., 36, 40-45.
30. Pickert,L. et al. (1998) Transcription regulatory region analysis using signal detection and fuzzy clustering. Bioinformatics, 14, 244-251.
31. Prestridge,D.S. (1996) SIGNAL SCAN 4.0: additional databases and sequence formats. Comput. Appl. Biosci., 12, 157-160.
32. Quandt,K. et al. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
33. Roulet,E. et al. (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol., 20, 831-835.
34. Sandelin,A. and Wasserman,W.W. (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol. Biol., 338, 207-215.
35. Sandelin,A. et al. (2004a) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32(Database issue), D91-D94.
36. Sandelin,A. et al. (2004b) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res., 32, W249-W252.
37. Sarsero,J.P. et al. (2004) Human BAC-mediated rescue of the Friedreich ataxia knockout mutation in transgenic mice. Mamm. Genome, 15, 370-382.
38. Schones,D.E. et al. (2005) Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics, 21, 307-313.
39. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
40. Tahirov,T.H. et al. (2001) Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta. Cell, 104, 755-767.
41. Thirunavukkarasu,K. et al. (2001) Stimulation of osteoprotegerin (OPG) gene expression by transforming growth factor-beta (TGF-beta). Mapping of the OPG promoter region that mediates TGF-beta effects. J. Biol. Chem., 276, 39241-39250.
42. Ufer,C. et al. (2003) Functional characterization of cis- and trans-regulatory elements involved in expression of phospholipid hydroperoxide glutathione peroxidase. Nucleic Acids Res., 31, 4293-4303.
43. Vanpoucke,G. et al. (2004) GATA-4 and MEF2C transcription factors control the tissue-specific expression of the alphaT-catenin gene CTNNA3. Nucleic Acids Res., 32, 4155-4165.
44. Venter,J.C. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
45. Werner,T. et al. (2003) Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J., 17, 1228-1237.
46. Willis,D.M. et al. (2002) Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. J. Biol. Chem., 277, 37280-37291.
47. Wolfertstetter,F. et al. (1996) Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comput. Appl. Biosci., 12, 71-80.
48. Ziegler-Heitbrock,L. et al. (2003) IFN-alpha induces the human IL-10 gene by recruiting both IFN regulatory factor 1 and Stat3. J. Immunol., 171, 285-290.