MODELS FOR COMPLEX EUKARYOTIC REGULATORY DNA SEQUENCES

Information Processing and Living Systems

Volumn , Issue , 2005, Pages 575-610

  Ohler, Uwe ^a   Frith, Martin C ^b,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 68049110237     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9781860946882_0003     Document Type: Chapter

References (158)

1. M. D. Adams, et al., The genome sequence of Drosophila melanogaster. Science 287(5461), 2185-2195 (2000)
2. S. Aerts, et al., Computational detection of cis-regulatory modules. Bioinformatics 19 Suppl 2, II5-II14 (2003)
3. S. Aerts, et al., Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res. 31(6), 1753-1764 (2003)
4. F. Antequera and A. Bird, Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA 90(24), 11995-11999 (1993)
5. S. Aparicio, et al., Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. USA 92(5), 1684-1688 (1995)
6. I. R. Arkhipova, Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics 139(3), 1359-1369 (1995)
7. M. I. Arnone and E. H. Davidson, The hardwiring of development: organization and function of genomic regulatory systems. Development 124(10), 1851-1864 (1997)
8. S. Audic and J. M. Claverie, Detection of eukaryotic promoters using Markov transition matrices. Comput. Chem. 21(4), 223-227 (1997)
9. V. N. Babenko, et al., Investigating extended regulatory regions of genomic DNA sequences. Bioinformatics 15(7-8), 644-653 (1999)
10. T. L. Bailey and W. S. Noble, Searching for statistically significant regulatory modules. Bioinformatics 19 Suppl 2, II16-II25 (2003)
11. V. B. Bajic and V. Brusic, Computational detection of vertebrate RNA polymerase II promoters. Methods Enzymol. 370, 237-250 (2003)
12. V. B. Bajic and S. H. Seah, Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res. 13(8), 1923-1929 (2003)
13. V. B. Bajic, et al., Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics 18(1), 198-199 (2002)
14. P. Baldi and S. Brunak, Bioinformatics: The Machine Learning Approach. 2 ed: Bradford (2001)
15. P. V. Benos, M. L. Bulyk and G. D. Stormo, Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res. 30(20), 4442-4451 (2002)
16. C. M. Bergman, et al., Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 3(12), RESEARCH0086 (2002)
17. B. P. Berman, et al., Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA 99(2), 757-762 (2002)
18. A. Bird, DNA methylation patterns and epigenetic memory. Genes Dev. 16(1), 6-21 (2002)
19. T. Blumenthal and K. S. Gleason, Caenorhabditis elegans operons: form and function. Nat. Rev. Genet. 4(2), 112-120 (2003)
20. D. Boffelli, M. A. Nobrega and E. M. Rubin, Comparative genomics at the vertebrate extremes. Nat. Rev. Genet. 5(6), 456-465 (2004)
21. R. J. Britten and E. H. Davidson, Gene regulation for higher cells: A theory. Science 165(891), 349-357 (1969)
22. P. Bucher, Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212(4), 563-578 (1990)
23. M. L. Bulyk, et al., Quantifying DNA-protein interactions by doublestranded DNA arrays. Nat. Biotechnol. 17(6), 573-577 (1999)
24. C. Burge and S. Karlin, Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268(1), 78-94 (1997)
25. J. E. Butler and J. T. Kadonaga, The RNA polymerase II core promoter: A key component in the regulation of gene expression. Genes Dev. 16(20), 2583-2592 (2002)
26. V. C. Calhoun and M. Levine, Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex. Proc. Natl. Acad. Sci. USA 100(17), 9878-9883 (2003)
27. R. A. Cameron, et al., Cis-Regulatory activity of randomly chosen genomic fragments from the sea urchin. Gene Expr. Patterns 4(2), 205-213 (2004)
28. S. Cawley, et al., Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4), 499-509 (2004)
29. G. E. Chalkley and C. P. Verrijzer, DNA binding site selection by RNA polymerase II TAFs: A TAF(II)250-TAF(II)150 complex recognizes the initiator. Embo J. 18(17), 4835-4845 (1999)
30. Q. K. Chen, G. Z. Hertz and G. D. Stormo, PromFD 1.0: A computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci. 13(1), 29-35 (1997)
31. J. M. Claverie and I. Sauvaget, Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput. Appl. Biosci. 1(2), 95-104 (1985)
32. C. E. Clayton, Life without transcriptional control? From fly to man and back again. Embo J. 21(8), 1881-1888 (2002)
33. P. Clote and R. Backofen, Computational Molecular Biology: An Introduction: John Wiley & Sons (2000)
34. D. E. Clyde, et al., A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature 426(6968), 849-853 (2003)
35. R. M. Coulson, N. Hall and C. A. Ouzounis, Comparative Genomics of Tran-scriptional Control in the Human Malaria Parasite Plasmodium falciparum. Genome Res. 14(8), 1548-1554 (2004)
36. E. M. Crowley, K. Roeder and M. Bina, A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol. 268(1), 8-14 (1997)
37. E. Davidson, Genomic Regulatory Systems: Development and Evolution: Academic Press (2001)
38. R. V. Davuluri, I. Grosse and M. Q. Zhang, Computational identification of promoters and first exons in the human genome. Nat. Genet. 29(4), 412-417 (2001)
39. E. T. Dermitzakis and A. G. Clark, Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19(7), 1114-1121 (2002)
40. T. A. Down and T. J. Hubbard, Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12(3), 458-461 (2002)
41. I. W. Duncan, Transvection effects in Drosophila. Annu. Rev. Genet. 36, 521-556 (2002)
42. R. Durbin, et al., Biological sequence analysis: Cambridge University Press (1998)
43. L. Duret and P. Bucher, Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7(3), 399-406 (1997)
44. L. Elnitski, et al., Distinguishing regulatory DNA from neutral sites. Genome Res. 13(1), 64-72 (2003)
45. A. Erives and M. Levine, Coordinate enhancers share common organizational features in the Drosophila genome. Proc. Natl. Acad. Sci. USA 101(11), 3851-3856 (2004)
46. K. A. Frazer, et al., Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13(1), 1-12 (2003)
47. K. A. Frazer, et al., Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14(3), 367-372 (2004)
48. K. Freeh, J. Danescu-Mayer and T. Werner, A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J. Mol. Biol. 270(5), 674-687 (1997)
49. M. C. Frith, U. Hansen and Z. Weng, Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17(10), 878-889 (2001)
50. M. C. Frith, M. C. Li and Z. Weng, Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31(13), 3666-3668 (2003)
51. M. C. Frith, et al., Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 30(14), 3214-3224 (2002)
52. M. C. Frith, et al., Finding functional sequence elements by multiple local alignment. Nucleic Acids Res. 32(1), 189-200 (2004)
53. M. C. Frith, et al., Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 32(4), 1372-1381 (2004)
54. M. Gardiner-Garden and M. Frommer, CpG islands in vertebrate genomes. J. Mol. Biol. 196(2), 261-282 (1987)
55. Y. H. Grad, et al., Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. Melanogaster and D. Pseudoobscura. Bioinformatics, (2004)
56. A. S. Halees, D. Leyfer and Z. Weng, PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 31(13), 3554-3559 (2003)
57. M. S. Halfon, et al., Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12(7), 1019-1028 (2002)
58. S. Hannenhalli and S. Levy, Promoter prediction in the human genome. Bioinformatics 17 Suppl 1, S90-96 (2001)
59. S. Hannenhalli and S. Levy, Predicting transcription factor synergism. Nucleic Acids Res. 30(19), 4278-4284 (2002)
60. N. Harafuji, D. N. Keys and M. Levine, Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc. Natl. Acad. Sci. USA 99(10), 6802-6805 (2002)
61. R. C. Hardison, Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16(9), 369-372 (2000)
62. R. C. Hardison, et al., Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13(1), 13-26 (2003)
63. S. I. Hashimoto, et al., 5’-end SAGE for the analysis of transcriptional start sites. Nat. Biotechnol. 22(9), 1146-1149 (2004)
64. A. Hochheimer and R. Tjian, Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev. 17(11), 1309-1320 (2003)
65. A. Hochheimer, et al., TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420(6914), 439-445 (2002)
66. H. Huang, et al., Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J. Comput. Biol. 11(1), 1-14 (2004)
67. G. B. Hutchinson, The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Appl. Biosci. 12(5), 391-398 (1996)
68. I. Ioshikhes, E. N. Trifonov and M. Q. Zhang, Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA 96(6), 2891-2895 (1999)
69. I. P. Ioshikhes and M. Q. Zhang, Large-scale human promoter mapping using CpG islands. Nat. Genet. 26(1), 61-63 (2000)
70. N. Jareborg, E. Birney and R. Durbin, Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res. 9(9), 815-824 (1999)
71. O. Johansson, et al., Identification of functional clusters of transcription factor binding motifs in genome sequences: The MSCAN algorithm. Bioinformatics 19 Suppl 1, 1169-1176 (2003)
72. S. Karlin and S. F. Altschul, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87(6), 2264-2268 (1990)
73. S. Knudsen, Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics 15(5), 356-361 (1999)
74. Y. V. Kondrakhin, et al., Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11(5), 477-488 (1995)
75. G. Kreiman, Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Res. 32(9), 2889-2900 (2004)
76. W. Krivan and W. W. Wasserman, A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11(9), 1559-1566 (2001)
77. A. K. Kutach and J. T. Kadonaga, The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell Biol. 20(13), 4754-4764 (2000)
78. T. Lagrange, et al., New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12(1), 34-44 (1998)
79. D. Latchman, Gene Regulation: A Eukaryotic Perspective. 4 ed: Nelson Thornes (2002)
80. T. I. Lee, et al., Transcriptional regulatory networks in Saccharomyces cere-visiae. Science 298(5594), 799-804 (2002). '
81. M. Levine and R. Tjian, Transcription regulation and animal diversity. Nature 424(6945), 147-151 (2003)
82. V. G. Levitsky, et al., Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics 17(11), 998-1010 (2001)
83. S. Levy and S. Hannenhalli, Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome 13(9), 510-514 (2002)
84. H. Li and W. Wang, Dissecting the transcription networks of a cell using computational genomics. Curr. Opin. Genet. Dev. 13(6), 611-616 (2003)
85. A. P. Lifanov, et al., Homotypic regulatory clusters in Drosophila. Genome Res. 13(4), 579-588 (2003)
86. C. Y. Lim, et al., The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18(13), 1606-1617 (2004)
87. S. Lisser and H. Margalit, Determination of common structural features in Escherichia coli promoters by computer analysis. Eur. J. Biochem. 223(3), 823-830 (1994)
88. R. Liu and D. J. States, Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Res. 12(3), 462-469 (2002)
89. R. Liu, R. C. McEachin and D. J. States, Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res. 13(4), 654-661 (2003)
90. G. G. Loots, et al., Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288(5463), 136-140 (2000)
91. M. Z. Ludwig, et al., Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403(6769), 564-567 (2000)
92. F. Lyko, DNA methylation learns to fly. Trends Genet 17(4), 169-172 (2001)
93. V. J. Makeev, et al., Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res. 31(20), 6016-6026 (2003)
94. M. Markstein, et al., Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 99(2), 763-768 (2002)
95. J. A. Martens, L. Laprade and F. Winston, Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429(6991), 571-574 (2004)
96. R. Martone, et al., Distribution of NF-kappaB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100(21), 12247-12252 (2003)
97. V. Matys, et al., TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31(1), 374-378 (2003)
98. S. Misra, et al., Annotation of the Drosophila melanogaster euchro-matic genome: A systematic review. Genome Biol. 3(12), RESEARCH0083 (2002)
99. R. O’Lone, et al., Genomic targets of nuclear estrogen receptors. Mol. Endocrinol. 18(8), 1859-1875 (2004)
100. D. T. Odom, et al., Control of pancreas and liver gene expression by HNF transcription factors. Science 303(5662), 1378-1381 (2004)
101. U. Ohler, Polygramme und Hidden Markov Modelle zur DNA-Sequenzanalyse, Friedrich-Alexander-Universitat: Erlangen (1995)
102. U. Ohler and H. Niemann, Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 17(2), 56-60 (2001)
103. U. Ohler, et al., Stochastic segment models of eukaryotic promoter regions. Pac. Symp. Biocomput. 380-391 (2000)
104. U. Ohler, et al., Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 17 Suppl 1, S199-206 (2001)
105. U. Ohler, et al., Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3(12), RESEARCH0087 (2002)
106. U. Ohler, et al., Interpolated markov chains for eukaryotic promoter recognition. Bioinformatics 15(5), 362-369 (1999)
107. U. Ohler, Computational Promoter Recognition in Eukaryotic Genomic DNA, Berlin: Logos (2002)
108. P. Pavlidis, et al., Promoter region-based classification of genes. Pac. Symp. Biocomput. 151-163 (2001)
109. A. G. Pedersen, et al., Characterization of prokaryotic and eukaryotic promoters using hidden Markov models. Proc. Int. Conf. Intell. Syst. Mol. Biol. 4, 182-191 (1996)
110. A. G. Pedersen, et al., DNA structure in human RNA polymerase II promoters. J. Mol. Biol. 281(4), 663-673 (1998)
111. L. A. Pennacchio and E. M. Rubin, Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2(2), 100-109 (2001)
112. D. S. Prestridge, Predicting Pol II promoter sequences using transcription factor binding sites. J. Mol. Biol. 249(5), 923-932 (1995)
113. D. S. Prestridge and C. Burks, The density of transcriptional elements in promoter and non-promoter sequences. Hum. Mol. Genet. 2(9), 1449-1453 (1993)
114. N. Rajewsky, et al., Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3(1), 30 (2002)
115. M. Rebeiz, N. L. Reeves and J. W. Posakony, SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. Proc. Natl. Acad. Sci. USA 99(15), 9888-9893 (2002)
116. M. G. Reese, Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26(1), 51-56 (2001)
117. M. G. Reese, et al., Genie-gene finding in Drosophila melanogaster. Genome Res. 10(4), 529-538 (2000)
118. S. Rombauts, et al., Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132(3), 1162-1176 (2003)
119. E. Roulet, et al., High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol. 20(8), 831-835 (2002)
120. P. J. Sabo, et al., Genome-wide identification of DNasel hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. USA 101(13), 4537-4542 (2004)
121. A. Sandelin and W. W. Wasserman, Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338(2), 207-215 (2004)
122. A. Sandelin, et al., JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32 Database issue, D91-94 (2004)
123. M. Scherf, A. Klingenhoff and T. Werner, Highly specific localization of promoter regions in large genomic sequences by Promoterlnspector: A novel context analysis approach. J. Mol. Biol. 297(3), 599-606 (2000)
124. M. Scherf, et al., First pass annotation of promoters on human chromosome 22. Genome Res. 11(3), 333-340 (2001)
125. C. D. Schmid, et al., The Eukaryotic Promoter Database EPD: The impact of in silico primer extension. Nucleic Acids Res. 32 Database issue, D82-85 (2004)
126. T. Shiraki, et al., Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 100(26), 15776-15781 (2003)
127. S. Sinha, E. Van Nimwegen and E. D. Siggia, A probabilistic method to detect regulatory modules. Bioinformatics 19 Suppl 1, 1292-1301 (2003)
128. S. T. Smale and J. T. Kadonaga, The RNA polymerase II core promoter. Annu. Rev. Biochem. 72, 449-479 (2003)
129. V. Solovyev and A. Salamov, The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5, 294-302 (1997)
130. V. V. Solovyev and I. A. Shahmuradov, PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res. 31(13), 3540-3545 (2003)
131. A. Sosinsky, et al., Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res. 31(13), 3589-3592 (2003)
132. G. D. Stormo and D. S. Fields, Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci. 23(3), 109-113 (1998)
133. X. Su, S. Wallenstein and D. Bishop, Nonoverlapping clusters: Approximate distribution and application to molecular biology. Biometrics 57(2), 420-426 (2001)
134. P. Sudarsanam, Y. Pilpel and G. M. Church, Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 12(11), 1723-1731 (2002)
135. Y. Sugahara, et al., Comparative evaluation of 5’-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene 263(1-2), 93-102 (2001)
136. L. V. Sun, et al., Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc. Natl. Acad. Sci. USA 100(16), 9428-9433 (2003)
137. Y. Suzuki, et al., DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res. 30(1), 328-331 (2002)
138. Y. Suzuki, et al., Construction and characterization of a full length-enriched and a 5’-end-enriched cDNA library. Gene 200(1-2), 149-156 (1997)
139. Y. Suzuki, et al., Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11(5), 677-684 (2001)
140. R. Tupler, G. Perini and M. R. Green, Expressing the human genome. Nature 409(6822), 832-833 (2001)
141. J. van Helden, Regulatory sequence analysis tools. Nucleic Acids Res. 31(13), 3593-3596 (2003)
142. C. P. Verrijzer and R. Tjian, TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem. Sci. 21(9), 338-342 (1996)
143. J. Vilo and K. Kivinen, Regulatory sequence analysis: Application to the interpretation of gene expression. Eur. Neuropsychopharmacol. 11(6), 399-411 (2001)
144. A. Wagner, Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15(10), 776-784 (1999)
145. W. W. Wasserman and J. W. Fickett, Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278(1), 167-181 (1998)
146. W. W. Wasserman and A. Sandelin, Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5(4), 276-287 (2004)
147. W. W. Wasserman, et al., Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 26(2), 225-228 (2000)
148. R. H. Waterston, et al., Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915), 520-562 (2002)
149. C. L. Wei, et al., 5’ Long serial analysis of gene expression (LongSAGE) and 3’ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl. Acad. Sci. USA 101(32), 11701-11706 (2004)
150. T. Werner, Identification and functional modelling of DNA sequence elements of transcription. Brief. Bioinform. 1(4), 372-380 (2000)
151. T. Werner, The state of the art of mammalian promoter recognition. Brief. Bioinform. 4(1), 22-30 (2003)
152. Q. Wu, et al., Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11(3), 389-404 (2001)
153. J. J. Wyrick and R. A. Young, Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev. 12(2), 130-136 (2002)
154. C. H. Yuh, H. Bolouri and E. H. Davidson, Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279(5358), 1896-1902 (1998)
155. C. H. Yuh, et al., Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246(1), 148-161 (2002)
156. M. Zavolan, et al., Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 13(6B), 1290-1300 (2003)
157. M. Q. Zhang, Identification of human gene core promoters in silico. Genome Res. 8(3), 319-326 (1998)
158. J. Zhu, J. S. Liu and C. E. Lawrence, Bayesian adaptive sequence alignment algorithms. Bioinformatics 14(1), 25-39 (1998)