Title

Position weight matrix model as a tool for the study of regulatory elements distribution across the DNA sequence

Journal title

Archives of Control Sciences

Yearbook

2010

Issue

No 4

Authors

Jaksik, Roman ; Rzeszowska-Wolny, Joanna

Divisions of PAS

Nauki Techniczne

Publisher

Committee of Automatic Control and Robotics PAS

Date

2010

Identifier

DOI: 10.2478/v10170-010-0028-1 ; ISSN 1230-2384

Source

Archives of Control Sciences; 2010; No 4

References

Gregory T. (2007), Eukaryotic genome size databases, Nucleic Acids Res, 35. ; Latchman D. (1997), Transcription factors: an overview, Int. J. Biochem. Cell Biol, 29, 1305. ; Karin M. (1990), Too many transcription factors: positive and negative interactions, New Biol, 2, 126. ; Roeder R. (1996), The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem. Sci, 21, 327. ; Nikolov D. (1997), RNA polymerase II transcription initiation: a structural view, Proc. Natl. Acad. Sci. USA, 94, 15. ; Lee T. (2000), Transcription of eukaryotic protein-coding genes, Annu. Rev. Genet, 34, 77. ; Babu M. (2004), Structure and evolution of transcriptional regulatory networks, Curr. Opin. Struct. Biol, 14, 283. ; Brivanlou A. (2002), Signal transduction and the control of gene expression, Science, 295, 813. ; Levine M. (2003), Transcription regulation and animal diversity, Nature, 424, 147. ; Barthel K. (2008), A transcriptional enhancer from the coding region of ADAMTS5, PLoS One, 3. ; Gill G. (2001), Regulation of the initiation of eukaryotic transcription, Essays Biochem, 37, 33. ; Narlikar G. (2002), Cooperation between complexes that regulate chromatin structure and transcription, Cell, 108, 475. ; Xu L. (1999), Coactivator and corepressor complexes in nuclear receptor function, Curr. Opin. Genet. Dev, 9, 140. ; Wong J. (1994), TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs, Nucleic Acids Res, 22, 1890. ; Mukumoto F. (1993), DNA sequence requirement of a TATA element-binding protein from Arabidopsis for transcription in vitro, Plant Mol. Biol, 23, 995. ; Day W. (1992), Critical comparison of consensus methods for molecular sequences, Nucleic Acids Res, 20, 5, 1093. ; Claverie J. (1996), The statistical significance of nucleotide positionweight matrix matches, Comput. Appl. Biosci, 12, 431. ; Stormo G. (1982), Characterization of translational initiation sites in E. coli, Nucleic Acids Res, 10, 2971. ; Sandelin A. (2004), ConSite: web-based prediction of regulatory elements using cross-species comparison, Nucleic Acids Res, 32. ; 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. ; Masuda K. (2005), Androgen receptor binding sites identified by a GREF_GATA model, J. Mol. Biol, 353, 763. ; Bernardi G. (2000), Isochores and the evolutionary genomics of vertebrates, Gene, 241, 3. ; Touzet H. (2007), Efficient and accurate P-value computation for Position Weight Matrices, Algorithms for Molecular Biology, 2, doi.org/10.1186/1748-7188-2-15 ; Zhang J. (2007), Computing exact P-values for DNA motifs, Bioinformatics, 23, 531. ; Barash Y. (2003), Modeling dependencies in protein-DNA binding sites, null, 28. ; Zhao X. (2005), Finding short DNA motifs using permuted Markov models, J. Comput. Biol, 12, 894. ; King O. (2003), A non-parametric model for transcription factor binding sites, Nucleic Acids Res, 31, doi.org/10.1093/nar/gng117 ; Lenhard B. (2002), TFBS: Computational framework for transcription factor binding site analysis, Bioinformatics, 18, 1135. ; Hertz G. (1990), Identification of consensus patterns in unaligned DNA sequences known to be functionally related, Comput. Appl. Biosci, 6, 81. ; Kel A. (2003), MATCH: A tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res, 31, 3576. ; Loots G. (2004), rVISTA 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Res, 32, doi.org/10.1093/nar/gkh383 ; Marinescu V. (2005), MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes, BMC Bioinformatics, 6, 79. ; Sandelin A. (2004), JASPAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Res, 32, doi.org/10.1093/nar/gkh012