High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions

PLoS Computational Biology

Volumn 6, Issue 9, 2010, Pages

  Agius, Phaedra ^a   Arvey, Aaron ^a   Chang, William ^a   Noble, William Stafford ^b   Leslie, Christina ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; FORECASTING; MAMMALS; PROBES; TRANSCRIPTION; YEAST;

GENOMICS; IN-VITRO; IN-VIVO; MICROARRAYS DATA; POSITION SPECIFIC SCORING MATRIX; PROTEIN-BINDING; SEQUENCE PATTERNS; SUPPORT VECTOR REGRESSION MODELS; TRANSCRIPTION FACTOR BINDING; VITRO AND IN VIVO;

TRANSCRIPTION FACTORS;

DNA; TRANSCRIPTION FACTOR;

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA BINDING; HUMAN; INFORMATION PROCESSING; INTERMETHOD COMPARISON; KERNEL METHOD; NONHUMAN; PREDICTION; PROTEIN BINDING; PROTEIN MICROARRAY; SCORING SYSTEM;

EID: 78049440479     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000916     Document Type: Article

References (21)

1. Fulton D, Sundararajan S, Badis G, Hughes T, Wasserman W, et al. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 10: R29.
2. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
3. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription- factor binding site specificities. Nature Biotechnol 12: 1249-1435.
4. Noble WS (2004) Support vector machine applications in computational biology, MIT Press, chapter 3. Computational Molecular Biology, Available: http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0262195097.
5. Leslie C, Eskin E, Cohen A, Weston J, Noble WS (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics 20: 467-76.
6. Kuang R, Ie E, Wang K, Wang K, Siddiqi M, et al. (2005) Remote protein homology detection and motif extraction using profile kernels. J Bioinform Comput Biol 3: 527-550.
7. Pavesi G, Mauri G, Pesole G (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17.
8. Liu XS, Brutlag D, Liu J (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnol 20: 835-839.
9. Zhu C, Byers K, McCord R, Shi Z, Berger M, et al. (2009) High-resolution DNA binding specificity analysis of yeast transcription factors. Genome Res 19: 556-566.
10. 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.
11. Newburger DE, Bulyk ML (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37: 77-82.
12. Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32: 878-887.
13. Chen X, Hughes TR, Morris Q (2007) RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics 23: i72-i79.
14. Chen X, Xu H, Yuan P, Fang F, Huss M, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117.
15. ENCODE (2010) ENCODE data at UCSC Genome Browser. Available: http://www.genome.gov/10005107. Unpublished.
16. Wallerman O, Motallebipour M, Enroth S, Patra K, Bysani MSR, et al. (2009) Molecular interactions between hnf4a, foxa2 and gabp identified at regulatory dna elements through chip-sequencing. Nucleic Acids Res 37: 7498.
17. Fraenkel E, Rould M, Chambers K, Pabo C (1998) Engrailed homeodomaindna complex at 2.2 a° resolution: a detailed view of the interface and comparison with other engrailed structures1. J Mol Biol 284: 351.
18. Kissinger C, Liu B, Martin-Blanco E, Kornberg T, Pabo C (1990) Crystal structure of an engrailed homeodomain-dna complex at 2.8 p resolution: A framework for understanding homeodomain-dna interactions. Cell 63: 579.
19. Bolotin E, Liao H, Ta TC, Yang C, Hwang-Verslues W, et al. (2009) Integrated approach for the identification of human HNF4a target genes using protein binding microarrays. Hepatology.
20. Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, et al. (2010) Evidence-ranked motif identification. Genome Biol 11: R19.
21. Kharchenko P, Tolstorukov M, Park P (2008) Design and analysis of chip-seq experiments for dna-binding proteins. Nature Biotechnol advanced online publication. pp 1351-1359.