Super paramagnetic clustering of DNA sequences

Journal of Biological Physics

Volumn 32, Issue 1, 2006, Pages 11-25

  Radjiman, Sugiarto ^a   Lianyi, Han ^a   Jian Sheng, Wang ^a   Chen, Yu Zong ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Cluster algorithm; Data clustering; DNA sequence; Promoters; Statistical physics; Transcription factor binding sites

Indexed keywords

DNA; OLIGONUCLEOTIDE; TETRANUCLEOTIDE; TRANSCRIPTION FACTOR; TRINUCLEOTIDE; UNCLASSIFIED DRUG;

ALGORITHM; ARTHROPOD; ARTICLE; BINDING SITE; CLASSIFICATION; CLUSTER ALGORITHM; CONSENSUS SEQUENCE; CORRELATION FUNCTION; DATA CLUSTERING; DNA SEQUENCE; EPSTEIN BARR VIRUS; FERROMAGNET; GENE EXPRESSION; GENE FUNCTION; HERPES SIMPLEX VIRUS 1; HOUSEKEEPING GENE; HUMAN; MAGNET; MONTE CARLO METHOD; NONHUMAN; PHYSICS; PRIORITY JOURNAL; PROMOTER REGION; SENDSEN WANG CLUSTER; SIMULATION; STATISTICS; SUPERPARAMAGNETIC CLUSTERING; TRANSCRIPTION FACTOR BINDING SITE; VERTEBRATE; VIRUS GENE;

ARTHROPODA; HUMAN HERPESVIRUS 1; HUMAN HERPESVIRUS 4; VERTEBRATA;

EID: 33645463889     PISSN: 00920606     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10867-006-2120-0     Document Type: Article

References (39)

1. Butler, J.E.F. and Kadonaga, J.T.: The RNA Polymerase II Core Promoter: A Key Component in The Regulation of Gene Expression, Genes and Development 16 (2002), 2583-2592.
2. Burden, S., Lin, Y.X. and Zhang, R.: Improving Promoter Prediction for the NNPP2.2 Algorithm: A Case Study Using E-Coli DNA Sequences, Bioinformatics 21 (2004), 601-607.
3. Chou, K.C.: Prediction of Protein Signal Sequences and Their Cleavage Sites, Proteins: Structure, Function, and Genetics 42 (2001), 136-139.
4. Davuluri, R.V., Suzuki, Y., Sugano, S. and Zhang, M.Q.: CART Classification of Human 5′ UTR Sequences, Genome Research 10 (2000), 1807-1816.
5. Ma, X.T., Qian, M.P. and Tang, H.X.: Predicting Polymerase II Core Promoters by Cooperating Transcription Binding Sites in Eukaryotic Genes, Acta Biochimica et Biophysica Sinica 36 (2004), 250-258.
6. Rhee, J.W., Yeo, S.S., Na, K.R. and Kim, S.K.: New Training Method for Computational Identification of Promoter, Genome Informatics 13 (2002), 293-294.
7. Trinklein, N.D., Aldred, S.J.F., Saldanha, A.J. and Myers, R.M.: Identification and Functional Analysis of Human Transcriptional Promoters, Genome Research 13 (2003), 308-312.
8. Zhu, Z., Pilpel, Y. and Church, G.M.: Computational Identification of Transcription Factor Binding Sites via a Transcription-Factor-Centric Clustering (TFCC) Algorithm, J. Molecular Biology 318 (2002), 71-81.
9. Schmid, C.D., Praz, V., Delorenzi, M., Périer, R. and Bucher, P.: The Eukaryotic Promoter Database EPD: The Impact of in Silico Primer Extension, Nucleic Acids Res. 32 (2004), D82-D85.
10. Domany, E.: Cluster Analysis of Gene Expression Data, J. Statistical Physics 110 (2003), 1117-1139.
11. Getz, G., Levine, E., Domany, E. and Zhang, M.Q.: Super-paramagnetic Clustering of Yeast Gene Expression Profiles, Physica A 279 (2000), 457-464.
12. Getz, G., Levine, E. and Domany, E.: Coupled Two-Way Clustering Analysis of Gene Microarray Data, PNAS 97 (2000), 12079-12084.
13. Getz, G., Gal, H., Notterman, D.A. and Domany, E.: Coupled Two-Way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data, Bioinformatics 19 (2003), 1079-1089.
14. Blatt, M., Wiseman, S. and Domany, E.: Super-Paramagnetic Clustering of Data, Physical Review Letters 76 (1996), 3251-3255.
15. Blatt, M., Wiseman, S. and Domany, E.: Clustering Data through an Analogy to the Potts Model, Advances in Neural Information Processing System 8 (1996), 416-422.
16. Blatt, M., Wiseman, S. and Domany, E.: Data Clustering Using a Model Granular Magnet, Neural Computation 9 (1997), 1805-1842.
17. Blatt, M., Wiseman, S. and Domany, E.: Super-paramagnetic Clustering of Data, Physical Review E 57 (1998), 3767-3783.
18. Swendsen, R.H. and Wang, J.-S.: Nonuniversal Critical Dynamics in Monte Carlo Simulation, Physical Review Letters 58 (1987), 86-88.
19. Wang, J.-S. and Swendsen, R.H.: Cluster Monte Carlo Algorithms, Physica A 167 (1990), 565-579.
20. Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale D.A., O'Donovan, C., Redaschi, N. and Yeh, L.S.: The Universal Protein Resource (UniProt), Nucleic Acids Res., 33 (2005), D154-D159.
21. Abe, T., Kanaya, S., Kinouchi, M., Ichiba, Y., Kozuki, T. and Ikemura, T.: Informatics for Unveiling Hidden Genome Signatures, Genome Research 13 (2003), 693-702.
22. Faisst, S. and Meyer, S.: Compilation of Vertebrate-Encoded Transcription Factors, Nucleic Acids Res. 20 (1992), 3-26.
23. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhäuser, R., Prüß, M., Schacherer, F., Thiele, S. and Urbach, S.: The TRANSFAC System on Gene Expression Regulation, Nucleic Acids Res. 29 (2001), 281-283.
24. FitzGerald, P.C., Shlyakhenko, A., Mir, A.A. and Vinson, C.: Clustering of DNA Sequences in Human Promoters, Genome Research 14 (2004), 1562-1574.
25. Mariño-Ramírez, L., Spouge, J.L., Kanga, G.C. and Landsman, D.: Statistical Analysis of Over-Represented Words on Human Promoter Sequences, Nucleic Acids Res. 32 (2004), 949-958.
26. Berg, J.M., Tymoczko, J.L. and Stryer, L.: Biochemistry, 5th ed. W.H. Freeman and Company, New York 2002.
27. Latchman, D.S.: Eukaryotic Transcription Factors, 4th eds. Academic Press, London, 2004.
28. Weis, L. and Reinberg, D.: Transcription by RNA Polymerase II Initiator Directed Formation of Transcription Competent Complexes, FASEB Journal 6 (1992), 3300-3309.
29. Murakami, K., Kojima, T. and Sakaki, Y.: Detection of Tissue Specific Genes by Putative Regulatory Motifs in Human Promoter Sequences, Genome Informatics 14 (2003), 408-409.
30. Larsen, F., Gundersen, G., Lopez, R. and Prydz, H.: CpG Islands as Gene Markers in The Human Genome, Genomics 13 (1992), 1095-1107.
31. Courey, A. J. and Tjian, R.: Analysis of Sp1 in vivo Reveals Multiple Transcriptional Domains, Including a Novel Glutamine-Rich Activation Motif, Cell 55 (1988), 887-898.
32. Dynan, W.S. and Tjian, R.: The Promoter-Specific Transcription Factor Sp1 Binds to Upstream Sequences in The SV40 Early Promoter, Cell 35 (1983), 79-87.
33. Kadonaga, J.T., Carner, K.R., Masiarz, F.R. and Tjian, R.: Isolation of cDNA Encoding Transcription Factor Sp1 and Functional Analysis of The DNA Binding Domain, Cell 51 (1987), 1079-1090.
34. Philipsen, S. and Suske, G.: A Tale of Three Fingers: The Family of Mammalian Sp/XKLF Transcription Factors, Nucleic Acids Res. 27 (1999), 2991-3000.
35. Nakamura, Y., Miura, K., Fujino, Y., Iwao, H., Ogita, S. and Yamanaka, S.: Evolution, Structure, and Expression of GNPI/Oscillin Orthologous Genes, Genomics 68 (2000), 179-186.
36. Yamabe, Y., Shimamoto, A., Goto, M., Yokota, J., Sugawara, M. and Furuichi, Y.: Sp1-Mediated Transcription of the Werner Helicase Gene Is Modulated by Rb and p53, Molecular and Cellular Biology 18 (1998), 6191-6200.
37. Eisenberg, E. and Levanon, E.Y.: Human Housekeeping Genes are Compact, Trends in Genetics 19 (2003), 362-365.
38. Hsiao, L.-L., Dangond, F., Yoshida, T., et al.: A Compendium of Gene Expression in Normal Human Tissues, Physiol. Genomics 7 (2001), 97-104.
39. Laux, G., Perricaudet, M. and Farrell, P.J.: A Spliced Epstein-Barr Virus Gene Expressed in Immortalized Lymphocytes is Created by Circularization of The Linear Viral Genome, EMBO Journal 7 (1988), 769-774.