Similarity queries for temporal toxicogenomic expression profiles

PLoS Computational Biology

Volumn 4, Issue 7, 2008, Pages

  Smith, Adam A ^a,b   Vollrath, Aaron ^b   Bradfield, Christopher A ^b   Craven, Mark ^a,b  

^a University of Wisconsin   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; INTERPOLATION; TOXICITY;

ALIGNMENT ALGORITHMS; EXPRESSION PROFILE; GENE EXPRESSION TIME SERIES; LOCAL ALIGNMENT; SIMILARITY QUERY; SPLINE INTERPOLATION; TIME WARPING; TIMES SERIES; TOXICOGENOMICS; WARPING ALGORITHMS;

TIME SERIES;

ALGORITHM; ARTICLE; CALCULATION; DATA BASE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; TOXICOGENETICS; ANIMAL; AUTOMATED PATTERN RECOGNITION; DRUG EFFECT; DRUG TOXICITY; GENETIC DATABASE; GENETICS; LIVER; METHODOLOGY; MOUSE; SEQUENCE ALIGNMENT; TIME;

ANIMALS; DATABASES, GENETIC; DRUG TOXICITY; GENE EXPRESSION PROFILING; LIVER; MICE; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ALIGNMENT; TIME FACTORS; TOXICOGENETICS;

EID: 48249137399     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000116     Document Type: Article

References (20)

1. Hayes K, Vollrath A, Zastrow G, McMillan B, Craven M, et al. (2005) EDGE: a centralized resource for the comparison, analysis and distribution of toxicogenomic information. Mol Pharmacol 67: 1360-1368.
2. Ernst J, Nau G, Bar-Joseph Z (2005) Clustering short time series gene expression data. Bioinformatics 21: i159-i168.
3. Sakoe H, Chiba S (1978) Dynamic programming algorithm optimization for spoken word recognition. IEEE Trans Acoust 26: 43-49.
4. Sankoff D, Kruskal J (1983) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Reading (Massachusetts): Addison-Wesley.
5. Thomas R, Rank D, Penn S, Zastrow G, Hay K, et al. (2001) Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol 60: 1189-1194.
6. Natsoulis G, Ghaoui LE, Lanckriet G, Tolley A, Leroy F, et al. (2005) Classification of a large microarray data set: algorithm comparison and analysis of drug signatures. Genome Res 15: 724-736.
7. Lamb J, Crawford E, Peck D, Modell J, Blat I, et al. (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes and disease. Science 313: 1929-1935.
8. Aach J, Church G (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics 17: 495-508.
9. Criel J, Tsiporkova E (2006) Gene time expression warper: a tool for alignment, template matching and visualization of gene expression time series. Bioinformatics 22: 251-252.
10. Liu X, Müller HG (2003) Modes and clustering for time-warped gene expression profile data. Bioinformatics 19: 1937-1944.
11. Bar-Joseph Z, Gerber G, Gifford D, Jaakkola T, Simon I (2003) Continuous representations of time-series expression data. J Comput Biol 10: 341-356.
12. Listgarten J, Neal R, Roweis S, Emili A (2005) Multiple alignment of continuous time series. In: Advances in Neural Information Processing Systems 17 Saul L, Weiss Y, Bottou L, eds. Cambridge (Massachusetts): MIT Press. pp 817-824.
13. Gaffney SJ, Smyth P (2005) Joint probabilistic curve clustering and alignment. In: Saul LK, Weiss Y, Bottou L, eds. Advances in Neural Information Processing Systems 17. Cambridge, MA: MIT Press. pp 473-480.
14. Nielsen NV, Carstensen JM, Smedsgaard J (1998) Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping. J Chromatogr A 805: 17-35.
15. Burge C, Karlin S (1997) Prediction of complete gene human genomic DNA. J Mol Biol 268: 78-94.
16. Schmidler S, Liu J, Brutlag D (2000) Bayesian protein secondary structure. J Comput Biol 7: 233-248.
17. Rogers D, Adams J (1989) Mathematical Elements Graphics. New York: McGraw-Hill.
18. Altschul S (1991) Amino acid substitution matrices information theoretic perspective. J Mol Biol 219: 555-565.
19. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Sequence Analysis: Probabilistic Models of Proteins Acids. Cambridge, UK: Cambridge University Press.
20. Ratanamahatana C, Keogh EJ (2005) Three myths time warping data mining. In: Proceedings of SIAM Conference on Data Mining. Philadelphia: SIAM. pp 506-510.