Predicting DNA-binding specificities of eukaryotic transcription factors

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Schröder, Adrian ^a   Eichner, Johannes ^a   Supper, Jochen ^a   Eichner, Jonas ^a   Wanke, Dierk ^a   Carsten, Henneges ^a   Zell, Andreas ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; DNA; DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA BINDING; DNA TRANSFER; EUKARYOTE; GENE FREQUENCY; GENE LOCATION; GENE TARGETING; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS; SUPPORT VECTOR MACHINE; ALGORITHM; ANIMAL; BINDING COMPETITION; BINDING SITE; BIOLOGY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MOUSE; PROTEIN BINDING; PROTEIN MOTIF; RAT; REPRODUCIBILITY;

EUKARYOTA; RATTUS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; BINDING, COMPETITIVE; COMPUTATIONAL BIOLOGY; DNA; DNA-BINDING PROTEINS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; RATS; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS;

EID: 78649761218     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013876     Document Type: Article

References (79)

1. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC (2008) The genomes on line database (gold) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36: D475-D479.
2. Baldi P, Chauvin Y, Hunkapiller T, McClure MA (1994) Hidden markov models of biological primary sequence information. Proc Natl Acad Sci U S A 91: 1059-1063.
3. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, et al. (2002) An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 3: RESEARCH0081.
4. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315: 233-237.
5. Newburger DE, Bulyk ML (2009) Uniprobe: an online database of protein binding microarray data on protein-dna interactions. Nucleic Acids Res 37:D77-D82.
6. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, et al. (2009) Diversity and complexity in dna recognition by transcription factors. Science 324: 1720-1723.
7. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, et al. (2003) Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31:374-378.
8. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007) Uniprotkb/swiss-prot: The manually annotated section of the uniprot knowledgebase. Methods Mol Biol 406: 89-112.
9. Liu XD, Liu PC, Santoro N, Thiele DJ (1997) Conservation of a stress response: human heat shock transcription factors functionally substitute for yeast hsf. EMBO J 16: 6466-6477.
10. Gerlt JA, Babbitt PC (2000) Can sequence determine function? Genome Biol 1: REVIEWS0005.
11. Prakash A, Tompa M (2005) Discovery of regulatory elements in vertebrates through comparative genomics. Nat Biotechnol 23: 1249-1256.
12. Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, et al. (1998) Predicting function: from genes to genomes and back. J Mol Biol 283: 707-725.
13. Bock C, Walter J, Paulsen M, Lengauer T (2007) Cpg island mapping by epigenome prediction. PLoS Comput Biol 3: e110.
14. Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, et al. (1999) Automated genome sequence analysis and annotation. Bioinformatics 15:391-412.
15. Kretschmann E, Fleischmann W, Apweiler R (2001) Automatic rule generation for protein annotation with the c4.5 data mining algorithm applied on swissprot. Bioinformatics 17: 920-926.
16. Hegyi H, Gerstein M (2001) Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res 11: 1632-1640.
17. Leontovich AM, Tokmachev KY, van Houwelingen HC (2008) The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem. BMC Bioinformatics 9: 31.
18. Engelhardt BE, Jordan MI, Muratore KE, Brenner SE (2005) Protein molecular function prediction by bayesian phylogenomics. PLoS Comput Biol 1: e45.
19. Jensen LJ, Gupta R, Staerfeldt HH, Brunak S (2003) Prediction of human protein function according to gene ontology categories. Bioinformatics 19:635-642.
20. Juncker A, Jensen L, Pierleoni A, Bernsel A, Tress M, et al. (2009) Sequencebased feature prediction and annotation of proteins. Genome Biol 10: 206.
21. Stegmaier P, Kel AE, Wingender E (2004) Systematic dna-binding domain classification of transcription factors. Genome Inform 15: 276-286.
22. von Hippel PH, Berg OG (1986) On the specificity of dna-protein interactions. PNAS 83: 1608-12.
23. Gerland U, Moroz JD, Hwa T (2002) Physical constraints and functional characteristics of transcription factor-dna interaction. Proc Natl Acad Sci U S A 99: 12015-12020.
24. Sarai A, Kono H (2005) Protein-dna recognition patterns and predictions. Annu Rev Biophys Biomol Struct 34: 379-398.
25. Foat BC, Morozov AV, Bussemaker HJ (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce. Bioinformatics 22: e141-e149.
26. Roider HG, Kanhere A, Manke T, Vingron M (2007) Predicting transcription factor affinities to dna from a biophysical model. Bioinformatics 23: 134-141.
27. Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, et al. (2006) The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7: R36.
28. Rodionov DA (2007) Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 107: 3467-3497.
29. Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, et al. (2010) ModuleMaster: a new tool to decipher transcriptional regulatory networks. Biosystems 99: 79-81.
30. Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B (2004) Jaspar: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32: D91-D94.
31. Alleyne TM, Castillona LP, Badis G, Talukder S, Berger MF, et al. (2009) Predicting the binding preference of transcription factors to individual dna kmers. Bioinformatics 25: 1012-1018.
32. Alamanova D, Stegmaier P, Kel A (2010) Creating pwms of transcription factors using 3d structure-based computation of protein-dna free binding energies. BMC Bioinformatics 11: 225.
33. Shental N, Weinshall D (2003) Learning distance functions using equivalence relations. pp 11-18.
34. Wingender E (1997) Classification of eukaryotic transcription factors. Mol Biol (Mosk) 31: 584-600.
35. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA (2008) Dbd-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res 36: D88-D92.
36. Pape UJ, Rahmann S, Vingron M (2008) Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics 24:350-357.
37. Mahony S, Auron PE, Benos PV (2007) Dna familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol 3: e61.
38. Pearson K (1901) On lines and planes of closest fit to systems of points in space. Philosophical Magazine 2: 559-572.
39. Zhou D, Weston J, Gretton A, Bousquet O, Schölkopf B (2004) Ranking on data manifolds. In: Advances in Neural Information Processing Systems 16. MIT Press.
40. Harrison CJ, Bohm AA, Nelson HC (1994) Crystal structure of the dna binding domain of the heat shock transcription factor. Science 263: 224-227.
41. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, et al. (2007) The atgenexpress global stress expression data set: protocols, evaluation and model data analysis of uv-b light, drought and cold stress responses. Plant J 50:347-363.
42. Supper J, Strauch M, Wanke D, Harter K, Zell A (2007) Edisa: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics 8: 334.
43. Akerfelt M, Trouillet D, Mezger V, Sistonen L (2007) Heat shock factors at a crossroad between stress and development. Ann N Y Acad Sci 1113: 15-27.
44. Mahony S, Golden A, Smith TJ, Benos PV (2005) Improved detection of dna motifs using a self-organized clustering of familial binding profiles. Bioinformatics 21 Suppl 1: i283-i291.
45. Narlikar L, Gordân R, Ohler U, Hartemink AJ (2006) Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics 22: e384-e392.
46. Piipari M, Down TA, Hubbard TJ (2010) Metamotifs-a generative model for building families of nucleotide position weight matrices. BMC Bioinformatics 11:348.
47. Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, et al. (2008) Aaindex: amino acid index database, progress report 2008. Nucleic Acids Res 36: D202-D205.
48. Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, et al. (2005) TOUCAN 2:the all-inclusive open source workbench for regulatory sequence analysis. Nucl Acids Res 33: W393-396.
49. Li H, Zhan M (2008) Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data. Bioinformatics 24: 1874-1880.
50. Loo PV, Aerts S, Thienpont B, Moor BD, Moreau Y, et al. (2008) ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol 9: R66.
51. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2008) Ensembl 2008. Nucleic Acids Res 36: D707-D714.
52. Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J (2008) Using rsat to scan genome sequences for transcription factor binding sites and cisregulatory modules. Nat Protoc 3: 1578-1588.
53. Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, et al. (2006) The yeastract database: a tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae. Nucleic Acids Res 34: D446-D451.
54. Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, et al. (2008) Jaspar, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36: D102-D106.
55. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory dna elements (place) database: 1999. Nucleic Acids Res 27: 297-300.
56. Kel A, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis O, et al. (2003) MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. Nucl Acids Res 31: 3576-3579.
57. Holland RCG, Down TA, Pocock M, Prlic A, Huen D, et al. (2008) Biojava: an open-source framework for bioinformatics. Bioinformatics 24: 2096-2097.
58. Saigo H, Vert JP, Ueda N, Akutsu T (2004) Protein homology detection using string alignment kernels. Bioinformatics 20: 1682-1689.
59. Leslie CS, Eskin E, Cohen A, Weston J, Noble WS (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics 20: 467-476.
60. Liao L, Noble WS (2003) Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol 10: 857-868.
61. Kopp J, Schwede T (2004) The swiss-model repository of annotated threedimensional protein structure homology models. Nucleic Acids Res 32:D230-D234.
62. Moll A, Hildebrandt A, Lenhof HP, Kohlbacher O (2005) Ballview: an objectoriented molecular visualization and modeling framework. J Comput Aided Mol Des 19: 791-800.
63. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics.
64. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, et al. (2006) Transfac and its module transcompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 1: 34: D108-D110.
65. Zhu J, Zhang MQ (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611.
66. Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, et al. (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4: 25.
67. Bergman CM, Carlson JW, Celniker SE (2005) Drosophila dnase i footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, drosophila melanogaster. Bioinformatics 21: 1747-1749.
68. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443-453.
69. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919.
70. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In Atlas of Protein Sequences and Structure 5: 345-352.
71. Lüthy R, McLachlan AD, Eisenberg D (1991) Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10: 229-239.
72. Mehta PK, Heringa J, Argos P (1995) A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Sci 4: 2517-2525.
73. Miyazawa S, Jernigan RL (1993) A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng 6: 267-278.
74. Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitutions in protein evolution. J Mol Evol 12: 219-236.
75. Niefind K, Schomburg D (1991) Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles. JMol Biol 219: 481-497.
76. Risler JL, Delorme MO, Delacroix H, Henaut A (1988) Amino acid substitutions in structurally related proteins. a pattern recognition approach. determination of a new and efficient scoring matrix. J Mol Biol 204: 1019-1029.
77. Wei L, Altman RB, Chang JT (1997) Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac Symp Biocomput. pp 465-476.
78. Saigo H, Vert JP, Akutsu T (2006) Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinformatics 7: 246.
79. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2008) Database resources of the national center for biotechnology information. Nucleic Acids Res 36: D13-D21.