A Platform for Processing Expression of Short Time Series (PESTS)

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Sinha, Anshu ^a   Markatou, Marianthi ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION PROFILES; INTERPRETABILITY; MULTIPLE TEST; NOVEL METHODS; RELEVANT FEATURES; SHORT TIME SERIES; SIGNIFICANCE ANALYSIS; VISUALIZATION FUNCTIONS;

TIME SERIES ANALYSIS;

GENE EXPRESSION;

ARTICLE; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; METHODOLOGY; TIME;

CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TIME FACTORS; USER-COMPUTER INTERFACE;

EID: 78651067356     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-13     Document Type: Article

References (31)

1. Filho JSS, Gilmour SG, Rosa GJM. Design of microarray experiments for genetical genomic studies. Genetics 2006, 174:945-957. 10.1534/genetics.106.057281, 1602072, 16888340.
2. Ribeiro CM, Hurd H, Wu Y, Martino MEB, Jones L, Brighton B, Boucher RC, O'neal WK. Azithromycin treatment alters gene expression in inflammatory lipid metabolism, and cell cycle pathways in well-differentiated human airway epithelia. PLoS 2009, 4(6):e5806.
3. Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW. Significance analysis of time course microarray experiments. PNAS 2005, 102(36):12837-12842. 10.1073/pnas.0504609102, 1201697, 16141318.
4. Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous Representations of Time-Series Gene Expression Data. Journal of Computational Biology 2003, 10(3-4):341-356. 10.1089/10665270360688057, 12935332.
5. Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time-series gene expression data. Bioinformatics 2005, 21(Suppl. 1):i159-i168. 10.1093/bioinformatics/bti1022, 15961453.
6. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
7. Park T, Yi SU, Lee S, Lee SY, Yoo D, Ahn J, Lee YS. Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics 2003, 19:694-703. 10.1093/bioinformatics/btg068, 12691981.
8. Wang J, Kim S. Global analysis of dauer gene expression in Caenorhabditis elegans. Development 2003, 130:1621-1634. 10.1242/dev.00363, 12620986.
9. Conesa A, Nueda MJ, Ferrer A, Talon M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics. 2006, 22(9):1096-1102.
10. Hong F, Li H. Functional hierarchical models for identifying genes with different time-course expression profiles. Biometrics 2005, 62:534-544.
11. Tusher V, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. PNAS 2001, 98:5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
12. Camillo B, Toffolo G, Nair SK, Greenlund LJ, Cobelli C. Significance analysis of microarray transcript levels in time series experiments. BMC Bioinformatics 2007, 8(Suppl 1):S10. 10.1186/1471-2105-8-S1-S10, 1885839, 17430554.
13. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96(6):2907-2912. 10.1073/pnas.96.6.2907, 15868, 10077610.
14. Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci USA 2002, 99:9121-9126. 10.1073/pnas.132656399, 12082179.
15. Schliep A, Schonhuth A, Steinhoff C. Using hidden Markov models to analyze gene expression time course data. Bioinformatics 2003, 19:i264-i272. 10.1093/bioinformatics/btg1036, 12855469.
16. Tchagang AB, Bui KV, McGinnis T, Benos PV. 2009 Extracting biologically significant patterns from short time series gene expression data. BMC Bioinformatics 2009, 10:255. 10.1186/1471-2105-10-255, 2743670, 19695084.
17. Ghandhi SA, Sinha A, Markatou M, Amundson SA. Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering. BMC Genomics 2011, 12(1):2.
18. Sinha A. Analyzing sparse and irregularly spaced time dependent gene expression data. 2010, Diss. Columbia University.
19. NAC Cressie Statistics for Spatial Data. 1993, Wiley, New York, 2, NAC Cressie.
20. Wilfrid DJ, Frank MJ. Introduction to Statistical Analysis. 1983, P377-P548. Dixon McGraw-Hill Book Company, New York, Wilfrid J, fourth.
21. Bonferroni CE. "Teoria statistica delle classi e calcolo delle probabilità.". 1936, 8:3-62. Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze.
22. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser 1995, B57:289-300.
23. Schweder T, Spjøvtoll E. Plots of p-values to evaluate many tests simultaneously. Biometrika 1982, 69:493-502.
24. Rousseeuw PJ. "Silhouettes: a Graphical Aid to the Interpretation and Validation of Cluster Analysis". Computational and Applied Mathematics 1987, 20:53-65.
25. Leek J, Monsen E, Dabney A, Storey J. EDGE: extraction and analysis of differential gene expression. Bioinformatics 2006, 22:507-508. 10.1093/bioinformatics/btk005, 16357033.
26. Conesa A, Nueda MJ, Ferrer A, Talon M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics. 2006, 22(9):1096-1102.
27. Serial Expression Analysis. , http://sea.bioinfo.cipf.es/
28. Peddada S, Harris S, Zajd J, Harvey E. ORIOGEN: order restricted inference for ordered gene expression data. Bioinformatics 2005, 21:3933-3934. 10.1093/bioinformatics/bti637, 16109745.
29. Ramoni M, Sebastiani P, Kohane I. Cluster analysis of gene expression dynamics. PNAS 2002, 99(14):9121-9126. 10.1073/pnas.132656399, 123104, 12082179.
30. Costa IG, Schonhuth A, Schliep A. The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinformatics 2005, 21(10):2544-2545. 10.1093/bioinformatics/bti311, 15701683.
31. Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 2006, 7:191. 10.1186/1471-2105-7-191, 1456994, 16597342.