References
This section is yet to be filled in. For now, relevant references are:
- Gang Su, Binchen Mao, and Jin Wang. A web server for transcription factor binding site prediction // Bioinformation.-2006.-1, 5.-P. 156-157.
- Zhao, F., Xuan, Z., Liu, L., and Zhang, M. Q. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies // Nucleic Acids Research.-2005.-33, suppl_1.-P. D103-D107.
- Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W. W., and Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles // Nucleic Acids Research.-2004.-32, suppl_1.-P. D91-D94.
- Lenhard, B. and Wasserman, W. W. TFBS: Computational framework for transcription factor binding site analysis // Bioinformatics.-2002.-18, 8.-P. 1135-1136.
- Schones, D. E., Sumazin, P., and Zhang, M. Q. Similarity of position frequency matrices for transcription factor binding sites // Bioinformatics.-2005.-21, 3.-P. 307-313.
- Stormo, G. D. DNA binding sites: representation and discovery // Bioinformatics.-2000.-16, 1.-P. 16-23.
- Staden, R. Computer methods to locate signals in nucleic acid sequences // Nucleic Acids Research.-1984.-12, 1Part2.-P. 505-519.
- Stormo, G. D., Schneider, T. D., Gold, L., and Ehrenfeucht, A. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli // Nucleic Acids Research.-1982.-10, 9.-P. 2997-3011.
- Hertz, G. Z. and Stormo, G. D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences // Bioinformatics.-1999.-15, 7.-P. 563-577.
- Hertz, G. Z., Hartzell, G. W., III, and Stormo, G. D. Identification of consensus patterns in unaligned DNA sequences known to be functionally related // Bioinformatics.-1990.-6, 2.-P. 81-92.
- Stormo, G. D. and Hartzell, G. W. Identifying Protein-Binding Sites from Unaligned DNA Fragments // Proceedings of the National Academy of Sciences.-1989.-86, 4.-P. 1183-1187.
- Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A. E., and Wingender, E. TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes // Nucleic Acids Research.-2006.-34, suppl_1.-P. D108-D110.
- Liu, X. S., Brutlag, D. L., and Liu, J. S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments // Nat Biotech.-2002.-20, 8.-P. 835-839.
- J.van Helden, B.Andre, and J.Collado-Vides. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies // J Mol Biol.-2006.-281, 5.-P. 827-842.
- Pilpel, Y., Sudarsanam, P., and Church, G. M. Identifying regulatory networks by combinatorial analysis of promoter elements // Nat Genet.-2001.-29, 2.-P. 153-159.
- Bussemaker, H. J., Li, H., and Siggia, E. D. Regulatory element detection using correlation with expression // Nat Genet.-2001.-27, 2.-P. 167-174.
- Furman, I. and Pilpel, Y. Promoting human promoters // Mol Syst Biol.-2006.-2,P. E1-E2.
- Zhang, M. Q. Computational prediction of eukaryotic protein-coding genes // Nature Reviews Genetics.-2002.-3, 9.-P. 698-709.
- Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., and Werner, T. MatInspector and beyond: promoter analysis based on transcription factor binding sites // Bioinformatics.-2005.-21, 13.-P. 2933-2942.
- Kel, A. E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V., and Wingender, E. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences // Nucleic Acids Research.-2003.-31, 13.-P. 3576-3579.
- Sandelin, A., Wasserman, W. W., and Lenhard, B. ConSite: web-based prediction of regulatory elements using cross-species comparison // Nucleic Acids Research.-2004.-32, suppl_2.-P. W249-W252.
- Curwen, V., Eyras, E., Andrews, T. D., Clarke, L., Mongin, E., Searle, S. M. J., and Clamp, M. The Ensembl Automatic Gene Annotation System // Genome Research.-2004.-14, 5.-P. 942-950.
- Jin, V. X., Leu, Y. W., Liyanarachchi, S., Sun, H., Fan, M., Nephew, K. P., Huang, T. H. M., and Davuluri, R. V. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray // Nucleic Acids Research.-2004.-32, 22.-P. 6627-6635.
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Bogdan Tokovenko, Rostyslav Golda, Protas Oleksiy.