Genome-wide in silico prediction of gene expression

Bioinformatics

Volumn 28, Issue 21, 2012, Pages 2789-2796

  McLeay, Robert C ^a   Lesluyes, Tom ^a,b   Cuellar Partida, Gabriel ^a   Bailey, Timothy L ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMPUTER SIMULATION; EMBRYONIC STEM CELL; GENE EXPRESSION; GENETIC ASSOCIATION; GENETICS; METABOLISM; METHODOLOGY; MOUSE; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN BINDING; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMPUTER SIMULATION; EMBRYONIC STEM CELLS; GENE EXPRESSION; GENOME-WIDE ASSOCIATION STUDY; HISTONES; LINEAR MODELS; MICE; MODELS, MOLECULAR; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84868020122     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts529     Document Type: Article

References (41)

1. Balakrishnan, L. and Milavetz, B. (2010) Decoding the histone h4 lysine 20 methy-lation mark. Crit. Rev. Biochem. Mol. Biol., 45, 440-33.
2. Barski, A. et al. (2009) Chromatin poises mirna-and protein-coding genes for expression. Genome Res., 19, 1742-33.
3. Berger, M.F. and Bulyk, M.L. (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat. Protoc., 4, 393-33.
4. Bernstein, B.E. et al. (2010) The nih roadmap epigenomics mapping consortium. Nat. Biotechnol., 28, 1045-33.
5. Bieda, M. et al. (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res., 16, 595-33.
6. Bolstad, B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-33.
7. Cao, R. et al. (2002) Role of histone h3 lysine 27 methylation in polycomb-group silencing. Science, 298, 1039-33.
8. Chen, X. et al. (2008) Integration of external signaling pathways with the core tran-scriptional network in embryonic stem cells. Cell, 133, 1106-33.
9. Cloonan, N. et al. (2008) Stem cell transcriptome profiling via massive-scale mrna sequencing. Nat. Methods, 5, 613-33.
10. Cuellar Partida, G. et al. (2012) Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics, 28, 56-33.
11. Das, D. et al. (2004) Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA, 101, 16234-33.
12. Das, D. et al. (2006) Adaptively inferring human transcriptional subnetworks. Mol. Syst. Biol., 2, 2006.0029.
13. ENCODE Project Consortium (2011). A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
14. Ernst, J. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-33.
15. Fejes, A.P. et al. (2008) Findpeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics, 24, 1729-33.
16. Gerstein, M.B. et al. (2010) Integrative analysis of the caenorhabditis elegans genome by the modencode project. Science, 330, 1775-33.
17. Grant, C.E. et al. (2011) Fimo: scanning for occurrences of a given motif. Bioinformatics, 27, 1017-33.
18. Karlic, R. et al. (2010) Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA, 107, 2926-33.
19. Kouzarides, T. (2007) Chromatin modifications and their function. Cell, 128, 693-33.
20. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biol., 10, R25.
21. Matys, V. et al. (2003) Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-33.
22. Meissner, A. et al. (2008) Genome-scale dna methylation maps of pluripotent and differentiated cells. Nature, 454, 766-33.
23. Mikkelsen, T.S. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-33.
24. Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-33.
25. Ouyang, Z. et al. (2009) Chip-seq of transcription factors predicts absolute and differential gene expression in mbryonic stem cells. Proc. Natl Acad. Sci. USA, 106, 21521-33.
26. Park, S.-J. and Nakai, K. (2011) A regression analysis of gene expression in es cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinformatics, 12 (Suppl. 1), S50.
27. Pasini, D. et al. (2010) Characterization of an antagonistic switch between histone h3 lysine 27 methylation and acetylation in the transcriptional regulation of poly-comb group target genes. Nucleic Acids Res., 38, 4958-33.
28. Portales-Casamar, E. et al. (2010) Jaspar 2010: The greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
29. R Development Core Team. (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-33.
30. Rosenbloom, K.R. et al. (2010) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res., 38, D620-D625.
31. Schnetz, M.P. et al. (2010) Chd7 targets active gene enhancer elements to modulate es cell-specific gene expression. PLoS Genet., 6, e1001023.
32. Schotta, G. et al. (2004) A silencing pathway to induce h3-k9 and h4-k20 trimethyla-tion at constitutive heterochromatin. Genes Dev., 18, 1251-33.
33. Trapnell, C. et al. (2009) Tophat: discovering splice junctions with RNA-seq. Bioinformatics, 25, 1105-33.
34. Valouev, A. et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods, 5, 829-33.
35. van Ingen, H. et al. (2008) Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure, 16, 1245-33.
36. Vaquerizas, J.M. et al. (2009) A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet., 10, 252-33.
37. Wang, Z. et al. (2008) Combinatorial patterns of histone acetylations and methyla-tions in the human genome. Nat. Genet., 40, 897-33.
38. Wasserman, W.W. and Sandelin, A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-33.
39. Whitington, T. et al. (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res., 37, 14-33.
40. Xie, X. et al. (2009) MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics, 25, 167-33.
41. Zhang, Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.