Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Yuan, Yuan ^a,b   Chen, Yi Ping P ^b   Ni, Shengyu ^a   Xu, Augix G ^a,c   Tang, Lin ^a   Vingron, Martin ^d   Somel, Mehmet ^a,c   Khaitovich, Philipp ^a,c  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b LA TROBE UNIVERSITY   (Australia)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^d MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; TIME SERIES;

BIOLOGICAL FEATURES; DEVELOPMENT AND APPLICATIONS; DYNAMIC TIME WARPING ALGORITHMS; FALSE POSITIVE RATES; OPTIMAL ALIGNMENTS; ORIGINAL ALGORITHMS; PARAMETERS ESTIMATED; SIMULATION PROCEDURES;

TIME SERIES ANALYSIS;

PRIMATES;

ADOLESCENT; ADULT; AGED; ALGORITHM; ANIMAL; ARTICLE; CEREBELLUM; CHILD; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; INFANT; MACACA MULATTA; METABOLISM; MIDDLE AGED; PAN TROGLODYTES; PREFRONTAL CORTEX; PRENATAL DEVELOPMENT; PRESCHOOL CHILD; PRIMATE; TIME;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; ALGORITHMS; ANIMALS; CEREBELLUM; CHILD; CHILD, PRESCHOOL; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; INFANT; MACACA MULATTA; MIDDLE AGED; PAN TROGLODYTES; PREFRONTAL CORTEX; PRIMATES; TIME; YOUNG ADULT;

EID: 80051786521     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-147     Document Type: Article

References (25)

1. Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ. Transcriptional regulation and function during the human cell cycle. Nat Genet 2001, 27(1):48-54. 10.1038/83751, 11137997.
2. White KP, Rifkin SA, Hurban P, Hogness DS. Microarray analysis of Drosophila development during metamorphosis. Science 1999, 286(5447):2179-2184. 10.1126/science.286.5447.2179, 10591654.
3. Papatsenko D, Levine M, Goltsev Y. Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol 2011, 9(1):e1000584. 10.1371/journal.pbio.1000584, 3026761, 21283609.
4. Ahmad I, Suits F, Hoekman B, Swertz MA, Byelas H, Dijkstra M, Hooft R, Katsubo D, van Breukelen B, Bischoff R, et al. A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinformatics 2011,
5. Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL. Time alignment algorithms based on selected mass traces for complex LC-MS data. J Proteome Res 2010, 9(3):1483-1495. 10.1021/pr9010124, 20070124.
6. Sheehy SP, Huang S, Parker KK. Time-warped comparison of gene expression in adaptive and maladaptive cardiac hypertrophy. Circ Cardiovasc Genet 2009, 2(2):116-124. 10.1161/CIRCGENETICS.108.806935, 2731432, 20031575.
7. Sakoe H, Chiba S. Dynamic-Programming Algorithm Optimization for Spoken Word Recognition. Ieee Transactions on Acoustics Speech and Signal Processing 1978, 26(1):43-49.
8. Sankoff D, Kruskal J. Time warps, String Edits, and Macromolecules: The theory and Practice of Sequence comparison. 1983, Addison-Wesley.
9. Aach J, Church GM. Aligning gene expression time series with time warping algorithms. Bioinformatics 2001, 17(6):495-508. 10.1093/bioinformatics/17.6.495, 11395426.
10. Goltsev Y, Papatsenko D. Time warping of evolutionary distant temporal gene expression data based on noise suppression. BMC Bioinformatics 2009, 10:353. 10.1186/1471-2105-10-353, 2771023, 19857268.
11. Smith AA, Vollrath A, Bradfield CA, Craven M. Similarity queries for temporal toxicogenomic expression profiles. PLoS Comput Biol 2008, 4(7):e1000116. 10.1371/journal.pcbi.1000116, 2453325, 18636114.
12. Criel J, Tsiporkova E. Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series. Bioinformatics 2006, 22(2):251-252. 10.1093/bioinformatics/bti787, 16293669.
13. Liu X, Muller HG. Modes and clustering for time-warped gene expression profile data. Bioinformatics 2003, 19(15):1937-1944. 10.1093/bioinformatics/btg257, 14555627.
14. Smith AA, Vollrath A, Bradfield CA, Craven M. Clustered alignments of gene-expression time series data. Bioinformatics 2009, 25(12):i119-127. 10.1093/bioinformatics/btp206, 2687960, 19477977.
15. Somel M, Franz H, Yan Z, Lorenc A, Guo S, Giger T, Kelso J, Nickel B, Dannemann M, Bahn S, et al. Transcriptional neoteny in the human brain. Proc Natl Acad Sci USA 2009, 106(14):5743-5748. 10.1073/pnas.0900544106, 2659716, 19307592.
16. de Magalhães JP, Costa J. A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol 2009, 22:1770-1774. 10.1111/j.1420-9101.2009.01783.x, 19522730.
17. Smith BH, Crummett TL, Brandt KL. Ages of eruption of primate teeth: A compendium for aging individuals and comparing life histories. Am J Phys Anthropol 1994, 37:177-231.
18. Langer J. The heterochronic evolution of primate cognitive development. Biological Theory 2005, 1(1):41-43.
19. Rice SH, . ed The role of heterochrony in primate brain evolution. In Human evolution through developmental change. 2002, Johns Hopkins Univ. Press, Baltimore, ed.
20. Green BWSPJ. Nonparametric regression and generalized linear models. 1994, CRC Press.
21. Erraji-Benchekroun L, Underwood MD, Arango V, Galfalvy H, Pavlidis P, Smyrniotopoulos P, Mann JJ, Sibille E. Molecular aging in human prefrontal cortex is selective and continuous throughout adult life. Biol Psychiatry 2005, 57(5):549-558. 10.1016/j.biopsych.2004.10.034, 15737671.
22. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 2008, 28(1):264-278. 10.1523/JNEUROSCI.4178-07.2008, 18171944.
23. Somel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, Yuan Y, Ning Z, Hu Y, Menzel C, et al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res 2010, 20(9):1207-1218. 10.1101/gr.106849.110, 2928499, 20647238.
24. Seress L, Ribak CE. Postnatal development and synaptic connections of hilar mossy cells in the hippocampal dentate gyrus of rhesus monkeys. J Comp Neurol 1995, 355(1):93-110. 10.1002/cne.903550111, 7543501.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.