Computational analyses of eukaryotic promoters

BMC Bioinformatics

Volumn 8, Issue SUPPL. 6, 2007, Pages

  Zhang, Michael Q ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ANALYSIS; COMPUTATIONAL APPROACH; EUKARYOTIC PROMOTERS; GENE EXPRESSION PROFILES; GENE REGULATION NETWORK; GENOMICS; MAX PLANCK INSTITUTE;

COMPUTATIONAL METHODS; GENE EXPRESSION;

NETWORKS (CIRCUITS);

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

BIOINFORMATICS; CHROMATIN STRUCTURE; COMPUTER ANALYSIS; CONSENSUS SEQUENCE; EPIGENETICS; EUKARYOTE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENOME ANALYSIS; GENOMICS; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PREDICTION; PROMOTER REGION; PROTEIN MOTIF; REVIEW; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME MAP; DNA SEQUENCE; GENETIC TRANSCRIPTION; GENETICS;

EUKARYOTA;

ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, GENETIC; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 38449108806     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S6-S3     Document Type: Review

References (57)

1. Smith AD Sumazin P Xuan Z Zhang MQ: DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci USA 2006, 103:6275-6280. 1458868 16606849 10.1073/pnas.0508169103
2. Zhang MQ: Computational Methods for Promoter Recognition. MIT Press, Cambridge, Massachusetts Jiang T, Xu Y, Zhang MQ 249-268.
3. Thomas MC Chiang CM: The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006, 41:105-78. 10.1080/ 10409230600648736 16858867
4. Jin VX Singer GA Agosto-Perez FJ Liyanarachchi S Davuluri RV: Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 2006, 7:114. 1475891 16522199 10.1186/1471-2105-7-114
5. Gershenzon NI Trifonov EN Ioshikhes IP: The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics 2006, 7:161. 1538597 16790048 10.1186/1471-2164-7-161
6. Lewis BA Sims RJ 3rd Lane WS Reinberg D: Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator. Mol Cell 2005, 18:471-481. 10.1016/ j.molcel.2005.04.005 15893730
7. Suzuki Y Yamashita R Sugano S Nakai K: DBTSS, DataBase of Transcriptional Start Sites: Progress Report 2004. Nucleic Acids Res 2004, 32:D78-81. 308810 14681363 10.1093/nar/gkh076
8. Maeda N Kasukawa T Oyama R Gough J Frith M Engstrom PG Lenhard B Aturaliya RN Batalov S Beisel KW Bult CJ Fletcher CF Forrest AR Furuno M Hill D Itoh M Kanamori-Katayama M Katayama S Katoh M Kawashima T Quackenbush J Ravasi T Ring BZ Shibata K Sugiura K Takenaka Y Teasdale RD Wells CA Zhu Y Kai C Kawai J Hume DA Carninci P Hayashizaki Y: Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet 2006, 2:e62: 1449903 16683036 10.1371/ journal.pgen.0020062
9. Carninci P Sandelin A Lenhard B Katayama S Shimokawa K Ponjavic J Semple CA Taylor MS Engstrom PG Frith MC Forrest AR Alkema WB Tan SL Plessy C Kodzius R Ravasi T Kasukawa T Fukuda S Kanamori-Katayama M Kitazume Y Kawaji H Kai C Nakamura M Konno H Nakano K Mottagui-Tabar S Arner P Chesi A Gustincich S Persichetti F Suzuki H Grimmond SM Wells CA Orlando V Wahlestedt C Liu ET Harbers M Kawai J Bajic VB Hume DA Hayashizaki Y: Genomewide analysis of mammalian promoter architecture and evolution. Nat Genet 2006, 38:626-635. 10.1038/ng1789 16645617
10. Schmid CD Perier R PrTz V Bucher P: EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res 2006, 34:D82-5. 1347508 16381980 10.1093/nar/gkj146
11. Gross P Oelgeschlager T: Core promoter-selective RNA polymerase II transcription. Biochem Soc Symp 2006, 73:225-36. 16626302
12. Bajic VB Tan SL Christoffels A Schonbach C Lipovich L Yang L Hofmann O Kruger A Hide W Kai C Kawai J Hume DA Carninci P Hayashizaki Y: Mice and men: Their promoter properties. PLoS Genet 2006, 2:e54. 1449896 16683032 10.1371/journal.pgen.0020054
13. Kim TH Ren B: Genome-Wide Analysis of Protein-DNA Interactions. Annu Rev Genomics Hum Genet 2006, 7:81-102. 10.1146/annurev.genom.7.080505.115634 16722805
14. Kim TH Barrera LO Zheng M Qu C Singer MA Richmond TA Wu Y Green RD Ren B: A high-resolution map of active promoters in the human genome. Nature 2005, 436:876-80. 10.1038/nature03877 15988478 1895599
15. Wasserman WW Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-87. 10.1038/nrg1315 15131651
16. Tompa M Li N Bailey TL Church GM De Moor B Eskin E Favorov AV Frith MC Fu Y Kent WJ Makeev VJ Mironov AA Noble WS Pavesi G Pesole G Regnier M Simonis N Sinha S Thijs G van Helden J Vandenbogaert M Weng Z Workman C Ye C Zhu Z: Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23:137-44. 10.1038/nbt1053 15637633
17. Hertz GZ Hartzell GW 3rd Stormo GD: Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 1990, 6:81-92. 2193692
18. Lawrence CE Reilly AA: An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 1990, 7:41-51. 10.1002/prot.340070105 2184437
19. Bailey TL Elkan C: The value of prior knowledge in discovering motifs with MEME. Proceedings of the International Conference on Intelligent Systems for Molecular Biology. 1995, 3:21-9.
20. Lawrence CE Altschul SF Boguski MS Liu JS Neuwald AF Wootton JC: Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-14. 10.1126/science.8211139 8211139
21. Zhang MQ: Computational Prediction of Eukaryotic Protein-Coding Genes. Nat Rev Genet 2002, 3(9):698-709. 10.1038/nrg890 12209144
22. Workman CT Stormo GD: ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pacific Symposium on Biocomputing 2002:467-78.
23. Sinha S: Discriminative motifs. J Comput Biol 2003, 10:599-615. 10.1089/ 10665270360688219 12935347
24. Sumazin P Chen G Hata N Smith AD Zhang T Zhang MQ: DWE: Discriminating word enumerator. Bioinformatics 2005, 21:31-8. 10.1093/bioinformatics/ bth471 15333453
25. Smith AD Sumazin P Zhang MQ: Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci USA 2005, 102:1560-5. 547828 15668401 10.1073/pnas.0406123102
26. Smith AD Sumazin P Das D Zhang MQ: Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics 2005, 21(Suppl 1):i403-12. 10.1093/bioinformatics/bti1043 15961485
27. Martinez MJ Smith AD Li B Zhang MQ Harrod KS: Computational prediction of novel components of lung transcriptional networks. Bioinformatics 2007, 23:21-29. 10.1093/bioinformatics/btl531 17050569
28. Smith AD Sumazin P Zhang MQ: Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol 2007, 3:73. 1800356 17224917 10.1038/ msb4100114
29. Hastie T Tibshirani R Friedman J: The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer, New York 2001
30. Bussemaker HJ Li H Siggia ED: Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-71. 10.1038/84792 11175784
31. Keles S van der Laan M Eisen MB: Identification of regulatory elements using a feature selection method. Bioinformatics 2002, 18:1167-75. 10.1093/bioinformatics/18.9.1167 12217908
32. Conlon EM XS Liu JD Lieb JS Liu: Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA 2003, 100:3339-44. 152294 12626739 10.1073/pnas.0630591100
33. Keles S van der Laan MJ Vulpe C: Regulatory motif finding by logic regression. Bioinformatics 2004, 20:2799-811. 10.1093/bioinformatics/ bth333 15166027
34. Friedman J: Multivariate adaptive regression splines. Ann Stat 1991, 19:1-141.
35. Das D Banerjee N Zhang MQ: Interacting models of cooperative gene regulation. Proc Natl Acad Sci USA 2004, 101:16234-9. 528978 15534222 10.1073/pnas.0407365101
36. Foat BC Morozov AV Bussemaker HJ: Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 2006, 22:e141-9. 10.1093/bioinformatics/btl223 16873464
37. Das D Nahle Z Zhang MQ: Adaptively inferring human transcriptional subnetworks. Mol Syst Biol 2006, 2. 2006.0029. Epub Jun 6 1681499 16760900
38. Hong P Liu XS Zhou Q Lu X Liu JS Wong WH: A boosting approach for motif modeling using ChIP-chip data. Bioinformatics 2005, 21:2636-43. 10.1093/ bioinformatics/bti402 15817698
39. Bajic VB Tan SL Suzuki Y Sugano S: Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004, 22:1467-73. 10.1038/nbt1032 15529174
40. Down TA Hubbard TJ: Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002, 12:458-61. 155284 11875034 10.1101/gr.216102
41. Ohler U Liao GC Niemann H Rubin GM: Computational analysis of core promoters in the Drosophila genome. Genome Biol 2002 3: RESEARCH0087. Epub 2002 Dec 20 151189 12537576
42. Davuluri RV Grosse I Zhang MQ: Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29(4):412-417. Erratum: Nat Genet 2002, 32(3):459. 10.1038/ng780 11726928
43. Bajic VB Seah SH: Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. Nucleic Acids Res 2003, 31:3560-3. 168976 12824365 10.1093/nar/gkg570
44. Matys V Kel-Margoulis OV 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 AE Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34:D108-10. 1347505 16381825 10.1093/nar/gkj143
45. Aonnenburg S Zien A Ratsch G: ARTS: accurate recognition of transcription starts in human. Bioinformatics 2006, 22:e472-80. 10.1093/ bioinformatics/btl250 16873509
46. Zhao X Xuan Z Zhang MQ: Boosting with stumps for predicting transcription start sites. Genome Biol 2007, 8(2):R17. 10.1186/ gb-2007-8-2-r17 17274821 1852414
47. Buck MJ Lieb JD: A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet 2006, 38:1446-51. 10.1038/ng1917 17099712
48. Huebert DJ Bernstein BE: Genomic views of chromatin. Curr Opin Genet Dev 2005, 15:476-81. 10.1016/j.gde.2005.08.001 16099159
49. Yuan GC Liu YJ Dion MF Slack MD Wu LF Altschuler SJ Rando OJ: Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005, 309:626-30. 10.1126/science.1112178 15961632
50. Rollins RA Haghighi F Edwards JR Das R Zhang MQ Ju J Bestor TH: Large-scale structure of genomic methylation patterns. Genome Res 2006, 16:157-63. 1361710 16365381 10.1101/gr.4362006
51. Schulze SR Wallrath LL: Gene Regulation by Chromatin Structure: Paradigms Established in Drosophila melanogaster. Annu Rev Entomol 2007, 52:171-92. 10.1146/annurev.ento.51.110104.151007 16881818
52. Cavalli G: Chromatin and epigeneticsBin development: blending cellular memory with cell fate plasticity. Development 2006, 133:2089-94. 10.1242/ dev.02402 16672331
53. Sabo PJ Kuehn MS Thurman R Johnson BE Johnson EM Cao H Yu M Rosenzweig E Goldy J Haydock A Weaver M Shafer A Lee K Neri F Humbert R Singer MA Richmond TA Dorschner MO McArthur M Hawrylycz M Green RD Navas PA Noble WS Stamatoyannopoulos JA: Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 2006, 3:511-8. 10.1038/ nmeth890 16791208
54. Heintzman ND Stuart RK Hon G Fu Y Ching CW Hawkins RD Barrera LO Van Calcar S Qu C Ching KA Wang W Weng Z Green RD Crawford GE Ren B: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007, 39:311-318. 10.1038/ng1966 17277777
55. Bock C Paulsen M Tierling S Mikeska T Lengauer T Walter J: CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet 2006, 2:e26. 1386721 16520826 10.1371/journal.pgen.0020026
56. Das R Dimitrova N Xuan Z Rollins RA Haghighi F Edwards JR Ju J Bestor TH Zhang MQ: Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci USA 2006, 103:10713-6. 1502297 16818882 10.1073/pnas.0602949103
57. Segal E Fondufe-Mittendorf Y Chen L Thastrom A Field Y Moore IK Wang JP Widom J: A genomic code for nucleosome positioning. Nature 2006, 442(7104):772-8. 10.1038/nature04979 16862119