MAPPER: A search engine for the computational identification of putative transcription factor binding sites in multiple genomes

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Marinescu, Voichita D ^a   Kohane, Isaac S ^a   Riva, Alberto ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS-REGULATORY MODULES; COMPUTATIONAL ANALYSIS; COMPUTATIONAL IDENTIFICATION; ENHANCED SENSITIVITY; MULTIPLE SEQUENCE ALIGNMENTS; PUTATIVE TRANSCRIPTION FACTORS; TEMPORAL EXPRESSIONS; TRANSCRIPTIONAL REGULATION;

COMPUTATIONAL METHODS; HIDDEN MARKOV MODELS; MAMMALS; QUERY PROCESSING; SEARCH ENGINES; YEAST;

GENES;

ESTROGEN RECEPTOR; GLUCOCORTICOID RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3; HEPATOCYTE NUCLEAR FACTOR 4; MYOCYTE ENHANCER FACTOR 2; NUCLEAR FACTOR I; PROTEIN P53; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E2F; CELL CYCLE PROTEIN; MCM5 PROTEIN, HUMAN; PROTEIN BINDING;

ACCURACY; BINDING SITE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; FLY; FUNGAL GENE; HUMAN; HUMAN GENOME; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DATABASE; REVIEW; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; TRANSCRIPTION REGULATION; WORM; YEAST; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER; COMPUTER LANGUAGE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; MOLECULAR EVOLUTION; NUCLEIC ACID DATABASE; PROBABILITY; PROCEDURES;

ALGORITHMS; ANIMALS; BASE SEQUENCE; BINDING SITES; CELL CYCLE PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTERS; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOME; HUMANS; INTERNET; MARKOV CHAINS; PROGRAMMING LANGUAGES; PROTEIN BINDING; SEQUENCE ALIGNMENT; SOFTWARE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; USER-COMPUTER INTERFACE;

EID: 25444517056     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-79     Document Type: Review

References (107)

1. Ghazi A, VijayRaghavan KV: Developmental biology. Control by combinatorial codes. Nature 2000, 408:419-420.
2. Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol 2003, 5:201.
3. Qiu P: Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun 2003, 309:495-501.
4. Pennacchio LA, Rubin EM: Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest 2003, 111:1099-1106.
5. Pennacchio LA, Rubin EM: Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2001, 2:100-109.
6. Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296:1205-1214.
7. Bailey TL, Elkan C: The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 1995, 3:21-29.
8. 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, 262:208-214.
9. Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
10. Buhler J, Tompa M: Finding motifs using random projections. J Comput Biol 2002, 9:225-242.
11. Brazma A, Jonassen I, Vilo J, Ukkonen E: Predicting gene regulatory elements in silico on a genomic scale. Genome Res 1998, 8:1202-1215.
12. Liu XS, Brutlag DL, Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20:835-839.
13. Workman CT, Stormo GD: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput 2000:467-478.
14. Bussemaker HJ, Li H, Siggia ED: Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci U S A 2000, 97:10096-10100.
15. Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z: Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res 2004, 32:1372-1381.
16. Thompson W, Rouchka EC, Lawrence CE: Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 2003, 31:3580-3585.
17. Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS: A suite of webbased programs to search for transcriptional regulatory motifs. Nucleic Acids Res 2004, 32:W204-7.
18. Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z: SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res 2004, 32:W235-41.
19. Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E: MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31:3576-3579.
20. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31:374-378.
21. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, 32 Database issue:D91-4.
22. Steffens NO, Galuschka C, Schindler M, Bulow L, Hehl R: AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res 2004, 32 Database issue:D368-72.
23. Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG: Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res 2002, 30:312-317.
24. Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV, Wingender E: TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res 2002, 30:332-334.
25. Levine M, Tjian R: Transcription regulation and animal diversity. Nature 2003, 424:147-151.
26. Bailey TL, Noble WS: Searching for statistically significant regulatory modules. Bioinformatics 2003, 19 Suppl 2:II16-II25.
27. Sinha S, Van Nimwegen E, Siggia ED: A probabilistic method to detect regulatory modules. Bioinformatics 2003, 19 Suppl 1:I292-I301.
28. Frith MC, Hansen U, Weng Z: Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 2001, 17:878-889.
29. Rajewsky N, Vergassola M, Gaul U, Siggia ED: Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 2002, 3:30.
30. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002, 99:757-762.
31. Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, Moor BD: Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res 2003, 31:1753-1764.
32. Frith MC, Spouge JL, Hansen U, Weng Z: Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res 2002, 30:3214-3224.
33. Sharan R, Ben-Hur A, Loots GG, Ovcharenko I: CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res 2004, 32:W253-6.
34. Alkema WB, Johansson O, Lagergren J, Wasserman WW: MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res 2004, 32:W195-8.
35. Dieterich C, Herwig R, Vingron M: Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. Bioinformatics 2003, 19 Suppl 2:II50-II56.
36. Sandelin A, Wasserman WW, Lenhard B: ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 2004, 32:W249-52.
37. Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S: Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 2004, 14:451-458.
38. Bigelow HR, Wenick AS, Wong A, Hobert O: CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. BMC Bioinformatics 2004, 5:27.
39. Loots GG, Ovcharenko I: rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res 2004, 32:W217-21.
40. Grad YH, Roth FP, Halfon MS, Church GM: Prediction of similarlyacting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura. Bioinformatics 2004.
41. Blanchette M, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 2002, 12:739-748.
42. Prakash A, Blanchette M, Sinha S, Tompa M: Motif discovery in heterogeneous sequence data. Pac Symp Biocomput 2004:348-359.
43. Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ: Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res 2002, 12:1408-1417.
44. Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW: Identification of conserved regulatory elements by comparative genome analysis. J Biol 2003, 2:13.
45. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE: Human-mouse genome comparisons to locate regulatory sites. Nat Genet 2000, 26:225-228.
46. Emberly EG, Rajewsky N, Siggia ED: Conservation of Regulatory Elements between two species of Drosophila. BMC Bioinformatics 2003, 4:57.
47. Stormo GD: DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
48. Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 2002, 30:4442-4451.
49. Man TK, Stormo GD: Non-independence of Mnt repressoroperator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res 2001, 29:2471-2478.
50. Bulyk ML, Johnson PL, Church GM: Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 2002, 30:1255-1261.
51. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
52. Durbin R, Eddy S, Krogh A, G. M: Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK, Cambridge University Press; 1998.
53. Hughey R, Krogh A: Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996, 12:95-107.
54. Grundy WN, Bailey TL, Elkan CP, Baker ME: Meta-MEME: motifbased hidden Markov models of protein families. Comput Appl Biosci 1997, 13:397-406.
55. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280.
56. Raman R, Overton GC: Application of hidden Markov modeling to the characterization of transcription factor binding sites. Proceedings of the 27th Hawaii International Conference on Systems Sciences 1994.
57. Yada T, Totoki Y, Ishikawa M, Asai K, Nakai K: Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 1998, 14:317-325.
58. Conkright MD, Guzman E, Flechner L, Su AI, Hogenesch JB, Montminy M: Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell 2003, 11:1101-1108.
59. Ellrott K, Yang C, Sladek FM, Jiang T: Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics 2002, 18 Suppl 2:S100-S109.
60. Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, Youngman P: Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 2001, 41:757-774.
61. Sandelin A, Wasserman WW: Prediction of nuclear hormone receptor response elements. Mol Endocrinol 2005, 19:595-606.
62. Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B: Genomic targets of the human c-Myc protein. Genes Dev 2003, 17:1115-1129.
63. Orian A, van Steensel B, Delrow J, Bussemaker HJ, Li L, Sawado T, Williams E, Loo LW, Cowley SM, Yost C, Pierce S, Edgar BA, Parkhurst SM, Eisenman RN: Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev 2003, 17:1101-1114.
64. Mirza A, Wu Q, Wang L, McClanahan T, Bishop WR, Gheyas F, Ding W, Hutchins B, Hockenberry T, Kirschmeier P, Greene JR, Liu S: Global transcriptional program of p53 target genes during the process of apoptosis and cell cycle progression. Oncogene 2003, 22:3645-3654.
65. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR: Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell 2004, 116:499-509.
66. Wasserman WW, Fickett JW: Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278:167-181.
67. Huang H, Kao MC, Zhou X, Liu JS, Wong WH: Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J Comput Biol 2004, 11:1-14.
68. Hermeking H, Lengauer C, Polyak K, He TC, Zhang L, Thiagalingam S, Kinzler KW, Vogelstein B: 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression. Mol Cell 1997, 1:3-11.
69. Jensen MR, Factor VM, Zimonjic DB, Miller MJ, Keck CL, Thorgeirsson SS: Chromosome localization and structure of the murine cyclin G1 gene promoter sequence. Genomics 1997, 45:297-303.
70. Utrera R, Collavin L, Lazarevic D, Delia D, Schneider C: A novel p53-inducible gene coding for a microtubule-localized protein with G2-phase-specific expression. Embo J 1998, 17:5015-5025.
71. Rebeiz M, Reeves NL, Posakony JW: 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 U S A 2002, 99:9888-9893.
72. Rohrbaugh M, Ramos E, Nguyen D, Price M, Wen Y, Lai ZC: Notch activation of yan expression is antagonized by RTK/pointed signaling in the Drosophila eye. Curr Biol 2002, 12:576-581.
73. Chen Y, Fischer WH, Gill GN: Regulation of the ERBB-2 promoter by RBPJkappa and NOTCH. J Biol Chem 1997, 272:14110-14114.
74. Eddy SR: HMMER User's Guide: Biological sequence analysis using profile hidden Markov models. 2003 [http://hmmer.wustl.edu].
75. Kelly KK, Meadows SM, Cripps RM: Drosophila MEF2 is a direct regulator of Actin57B transcription in cardiac, skeletal, and visceral muscle lineages. Mech Dev 2002, 110:39-50.
76. Wang DZ, Valdez MR, McAnally J, Richardson J, Olson EN: The Mef2c gene is a direct transcriptional target of myogenic bHLH and MEF2 proteins during skeletal muscle development. Development 2001, 128:4623-4633.
77. Shin HM, Han TH: CD28-mediated regulation of the c-jun promoter involves the MEF2 transcription factor in Jurkat T cells. Mol Immunol 1999, 36:197-203.
78. Frith MC, Hansen U, Spouge JL, Weng Z: Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 2004, 32:189-200.
79. Frech K, Quandt K, Werner T: Software for the analysis of DNA sequence elements of transcription. Comput Appl Biosci 1997, 13:89-97.
80. Krivan W, Wasserman WW: A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11:1559-1566.
81. Barash Y, Elidan G, Friedman N, Kaplan T: Modeling dependencies in protein-DNA binding sites: . In Seventh annual international conference in computational molecular biology (RECOMB) Berlin, Germany; 2003:28-37.
82. Gribskov M, Robinson N: Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996, 20:25-33.
83. Hennessy KM, Botstein D: Regulation of DNA replication during the yeast cell cycle. Cold Spring Harb Symp Quant Biol 1991, 56:279-284.
84. Dyson N: The regulation of E2F by pRB-family proteins. Genes Dev 1998, 12:2245-2262.
85. Trimarchi JM, Lees JA: Sibling rivalry in the E2F family. Nat Rev Mol Cell Biol 2002, 3:11-20.
86. Takahashi Y, Rayman JB, Dynlacht BD: Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression. Genes Dev 2000, 14:804-816.
87. Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ: Target gene specificity of E2F and pocket protein family members in living cells. Mol Cell Biol 2000, 20:5797-5807.
88. Ohtani K, Iwanaga R, Nakamura M, Ikeda M, Yabuta N, Tsuruga H, Nojima H: Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F. Oncogene 1999, 18:2299-2309.
89. Schuster-Bockler B, Schultz J, Rahmann S: HMM Logos for visualization of protein families. BMC Bioinformatics 2004, 5:7.
90. Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
91. Sinha S, Tompa M: Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res 2002, 30:5549-5560.
92. Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M: Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 1997, 266:231-245.
93. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
94. UCSC Genome Bioinformatics Sequence and Annotation Downloads [http://hgdownload.cse.ucsc.edu/downloads.html]
95. HomoloGene [ftp://ftp.ncbi.nih.gov/pub/HomoloGene/]
96. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31:28-33.
97. UCSC Genome Bioinformatics Table Browser [http://genome.ucsc.edu/cgi-bin/hgTables]
98. Siepel A, Haussler D: Phylogenetic hidden Markov models. In Statistical Methods in Molecular Evolution Edited by: Nielsen R. , Springer; 2004.
99. MEME/MAST Download [http://meme.sdsc.edu/meme/website/meme-download.html]
100. JASPAR Sites Download [http://jaspar.cgb.ki.se/DOWNLOAD/SITES/]
101. GLAM Datasets [http://zlab.bu.edu/glam/sup/]
102. Software for the Analysis of DNA Sequence Elements of Transcription http://anthea.gsf.de/biodv/review/definition_data.html
103. A Predictive Model for Regulatory Sequences Directing Liver-specific Transcription, Supplementary Material [http://www.cgb.ki.se/krivan/liver/liver.html]
104. RSA-tools - Patser [http://rsat.ulb.ac.be/rsat/patser_form.cgi]
105. Sequence Analysis: Local Markov Method [http://www-personal.umich.edu/~mckao/website/index_files/Projects.html]
106. AlignACE Accessory Software [http://atlas.med.harvard.edu/download/extra.html]
107. Marinescu VD, Kohane IS, Riva A: The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 2005, 33(Database):D91-7.