Integrated databases and computer systems for studying eukaryotic gene expression

Bioinformatics

Volumn 15, Issue 7-8, 1999, Pages 669-686

  Kolchanov, N A ^a   Ponomarenko, M P ^a   Frolov, A S ^a   Ananko, E A ^a   Kolpakov, F A ^a   Ignatieva, E V ^a   Podkolodnaya, O A ^a   Goryachkovskaya, T N ^a   Stepanenko, I L ^a   Merkulova, T I ^a   Babenko, V V ^a   Ponomarenko, Yu V ^a   Kochetov, A V ^a   Podkolodny, N L ^b   Vorobiev, D V ^a   Lavryushev, S V ^a   Grigorovich, D A ^a   Kondrakhin, Yu V ^a   Milanesi, L ^c   Wingender, E ^d   Solovyev, V ^e   Overton, G C ^f   more..

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b INSTITUTE OF COMPUTATIONAL MATHEMATICS AND MATHEMATICAL GEOPHYSICS   (Russian Federation)

^c Ist Tecnologie Biomediche Avanzate   (Italy)

^d HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; REGULATOR PROTEIN;

COMPUTER PROGRAM; COMPUTER SYSTEM; CONFERENCE PAPER; DATA BASE; DNA CONFORMATION; EUKARYOTE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SEQUENCE; INTERNET; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; RNA STRUCTURE; SIGNAL TRANSDUCTION; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION;

EUKARYOTA;

EID: 0032823191     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.7.669     Document Type: Conference Paper

References (40)

1. Afonnikov, D.A., Kondrakhin, Yu.V. and Titov, I.I. (1997) Revealing of correlated positions of the DNA-binding region of the CREB and AP-1 transcription factor families. Mol. Biol. (USSR), 31, 741-748.
2. Babenko, V.N., Kosarev, P.S., Vishnevsky, O.V., Levitsky, V.G., Basin, V.V. and Frolov, A.S. (1999) Investigating extended regulatory regions of genomic DNA sequences. Bioinformatics, 15, 644-653.
3. Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
4. 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.
5. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
6. Chen, Q., Hertz, G. and Stormo, G. (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.
7. Coleman, R.A. and Pugh, B.F. (1995) Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J. Biol. Chem., 270, 13850-13859.
8. Etzold, T., Ulyanov, A. and Argos, P. (1996) SRS: information retrieval system for molecular biology data banks. Methods Enzymol., 266, 114.
9. Fishburn, P.C. (1970) Utility Theory for Decision Making. John Wiley & Sons, New York.
10. Frech, K., Quandt, K. and Werner, T. (1997). Software for the analysis of DNA sequence elements of transcription. Comput. Appl. Biosci., 13, 89-97.
11. Frolov, A.S., Lavryushev, S.V., Vorobiev, D.G. and Grigorovich, D.A. (1998) A system for activation of the TRRD database: further development of GeneExpress. In Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk, August 24-31, pp. 136-138.
12. Gallie, D.R (1996) Translational control of cellular and viral mRNAs. Plant Mol. Biol., 32, 145-158.
13. Ischenko, I.V., Kochetov, A.V. Kel, A.E., Kisselev, L.L. and Kolchanov, N.A. (1996) Comparative analysis of the local secondary structure of mRNAs encoded by high and low-expression eukaryotic genes. In Computer Science and Biology. Proceedings of the German Conference on Bioinformatics. Leipzig, pp. 124-129.
14. Juo, Z.S., Chiu, T.K., Leiberman, P.M., Baikalov, I., Berk, A.J. and Dickerson, R.E. (1996) How proteins recognize the TATA box. J. Mol. Biol., 261, 239-254.
15. Karlin, S. and Brendel, V. (1992) Chance and statistical significance in protein and DNA sequence analysis. Science, 257, 39-49.
16. Kel, A.E., Kondrachin, Y.V., Kolpakov, Ph.A., Kel, O.V., Romashenko, A.G., Wingender, E., Milanesi, L. and Kolchanov, N.A. (1995) Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences In Proceedings of the Third International Conference on Intellegent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 197-205.
17. Klingmuller, U. (1997) The role of tyrosine phosphorylation in proliferation and maturation of erythroid progenitor cells - signals emanating from the erythropoietin receptor. Eur. J. Biochem., 249, 637-647.
18. Kochetov, A.V., Ischenko, I.V., Vorobiev, D.G., Kel, A.E., Babenko, V.N., Kisselev, L.L. and Kolchanov, N.A. (1998) Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features. FEBS Lett., 440, 351-355.
19. Kochetov, A.V., Ponomarenko, M.P., Frolov, A.S., Kisselev, L.L. and Kolchanov N.A. (1999) Prediction of eukaryotic mRNA translational properties. Bioinformatics, 15, 704-712.
20. Kolchanov, N.A. et al. (1998a) GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Montreal, Quebec, Canada, June 28-July 1, pp. 95-104.
21. Kolchanov, N.A., Ponomarenko, M.P., Ponomarenko, Yu.V., Podkolodny, N.L. and Frolov, A.S. (1998b) Functional sites in the prokaryotic and eukaryotic genomes: Computer models and activity predictions. Mol. Biol. (USSR), 32, 255-267.
22. Kolchanov, N.A. et al. (1999) Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res., 27, 303-306.
23. Kolpakov, F.A. and Ananko, E.A. (1999) Interactive data input into the GeneNet database through the Internet. Bioinformatics, 15, 713-714.
24. Kozak, M. (1994) Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie, 76, 815-821.
25. Lawrence, Ch.E., Altshul, S.F., Boguski, M.S., Liu, S.L., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
26. Levitsky, V.G., Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S. and Kolchanov, N.A. (1999) Nucleosomal DNA property database. Bioinformatics, 15, 582-592.
27. Mufson, R.A. (1997) The role of serine/threonine phosphorylation in hematopoietic cytokine receptor signal transduction. FASEB J., 11, 37-44.
28. Pain, V. (1996) Initiation of protein synthesis in eukaryotic cells. Eur. J. Biochem., 236, 747-771.
29. Perier, R.C., Junier, T., Bonnard, C. and Bucher, P. (1999) The Eukaryotic Promoter Database (EPD): recent developments. Nucleic Acids Res., 27, 307-309.
30. Ponomarenko, J.V. Ponomarenko, M.P., Frolov, A.S., Vorobyev, D.G., Overton, G.C. and Kolchanov, N.A. (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 654-668.
31. Ponomarenko, M.P., Ponomarenko, J.V., Kel, A.E. and Kolchanov, N.A. (1997a) Computer analysis of conformational features of the eukaryotic TATA-box DNA promoters. Mol. Biol. (USSR), 31, 733-740.
32. Ponomarenko, M.P., Kolchanova, A.N. and Kolchanov, N.A. (1997b) Generating programs for predicting the activity of functional sites. J. Comput. Biol., 4, 83-90.
33. Ponomarenko, M.P., Frolov, A.S., Ponomarenko, J.V., Podkolodnaya, O.A., Vorobiev, D.G. and Kolchanov, N.A. (1998) Mean Recognition: a systemic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. In Proceedings of World Multiconference on Systemics. Cybernetics and Informatics. Orlando, Florida, July 12-16, Vol. 4, pp. 224-230.
34. Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S., Podkolodny, N.L., Savinkova, L.K., Kolchanov, N.A. and Overton, G.C. (1999a) Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics, 15, 687-703.
35. Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S., Podkolodnaya, O.A., Vorobyev, D.G., Kolchanov, N.A. and Overton G.C. (1999b) Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinformatic, 15, 631-643.
36. Quandt, K., Frech, K., Herrmann, G. and Werner, T. (1995) A consensus match scoring system that is correlated with biological functionality. In Schomburg, D. and Lessel, U. (eds), Nucleic Acids and Proteins to Cell Metabolism. GBF Monographs, 18. VCH Publishers, New York, pp. 47-57.
37. Ray, B.K., Brendler, T.G., Adya, S., Daniels-McQeen, S., Miller, J.K., Hershey, J.W.B., Grifo, J.A., Merrick, W.C. and Thach, R.E. (1983) Role of mRNA competition in regulating translation: further characterization of mRNA discriminatory initiation factors. Proc. Natl Acad. Sci. USA, 80, 663-667.
38. Titov, I.I., Ivanisenko, V.A. and Kolchanov, N.A. (1998) Predicting RNA folding by genetic algorithm with local exhaustion. In Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk, August 24-31, p. 296.
39. Uberbacher, E.C., Xu, Y. and Mural, R.J. (1996) Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol., 266, 259-281.
40. Vorobiev, D.G., Ponomarenko, J.V. and Podkolodnaya, O.A. (1998) SAMPLES and ALIGNED: databases for functional site sequences. In Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk, August 24-31, pp 409-412.