STEM: A tool for the analysis of short time series gene expression data

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Ernst, Jason ^a   Bar Joseph, Ziv ^a  

^a Carnegie Mellon University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF DATA; BIOLOGICAL INTERPRETATION; BIOLOGICAL PROCESS; GENE EXPRESSION ANALYSIS; MICROARRAY EXPERIMENTS; SHORT TIME SERIES; TIME SERIES MICROARRAYS; TIME-SERIES EXPERIMENTS;

BIOLOGICAL MATERIALS; DATA VISUALIZATION; EXPERIMENTS; GENE EXPRESSION; TIME SERIES; TIME SERIES ANALYSIS; TOOLS;

DATA INTEGRATION;

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; COMPUTER AIDED DESIGN; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; HUMAN; INFORMATION RETRIEVAL; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; RAT; SERIAL ANALYSIS OF GENE EXPRESSION; SHORT TIME SERIES EXPRESSION MINER; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA MICROARRAY; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; PROCEDURES; SIGNAL TRANSDUCTION; TIME;

TRANSCRIPTION FACTOR;

CLUSTER ANALYSIS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; SIGNAL TRANSDUCTION; SOFTWARE; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 33646344978     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-191     Document Type: Article

References (27)

1. Spellman PT, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9(12):3273-97.
2. Arbeitman M, Furlong E, Imam F, Johnson E, Null B, Baker B, Krasnow M, Scott M, Davis R, White K: Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297:2270-75.
3. Guillemin K, Salama N, Tompkins L, Falkow S: Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. Proc Natl Acad Sci USA 2002, 99:15136-15141.
4. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R: NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 2005:D562-D566.
5. Ernst J, Nau G, Bar-Joseph Z: Clustering Short Time Series Gene Expression Data. Bioinformatics 2005, 21(Suppl 1):i159-i168.
6. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29.
7. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. PNAS 1998, 95(25):14863-14868.
8. S T, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nature Genetics 1999, 22(3):281-285.
9. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander E, Golub T: Interpreting patterns of gene expression with self organizing maps: Methods and applications to hematopoietic differentiation. PNAS 1999, 96:2907-2912.
10. 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.
11. Ramoni M, Sebastiani P, Kohane I: Cluster analysis of gene expression dynamics. PNAS 2002, 99(14):9121-9126.
12. STEM: Short Time-series Expression Miner [http://www.cs.cmu.edu/~jernst/ stem]
13. Bederson BB, Grosjean J, Meyer J: Toolkit Design for Interactive Structured Graphics. IEEE Transactions on Software Engineering 2004, 30(8):535-546.
14. The Gene Ontology [http://www.geneontology.org]
15. Gene Ontology Annotation EBI [http://www.ebi.ac.uk/GOA/]
16. Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21:3587-3595.
17. Jorgensen E, Dozmorov I, Frank M, Centola M, Albino A: Global gene expression analysis of human bronchial epithelial cells treated with tobacco condensates. Cell Cycle 2004, 3:1154-1168.
18. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R: EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinformatics 2005, 6:232.
19. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
20. Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN: High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiplemicroarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 2005, 6:.
21. Tusher V, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. PNAS 2001, 98:5116-5121.
22. Leek J, Monsen E, Dabney A, Storey J: EDGE: extraction and analysis of differential gene expression. Bioinformatics 2006, 22:507-508.
23. Wichert S, Fokianos K, Strimmer K: Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 2004, 20:5-20.
24. Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B: Dynamic Querying for Pattern Identification in Microarray and Genomic Data. Proceedings of the IEEE Multimedia Conference and Expo 2003 [http://ieeexplore.ieee.org/ie15/8655/27434/01221346.pdf?arnumber= 1221346].
25. Criel J, Tsiporkova E: Gene Time Expression Warper: a tool for alignment, template matching and visualization of gene expression time series. Bioinformatics 2005, 22:251-252.
26. Peddada S, Harris S, Zajd J, Harvey E: ORIOGEN: order restricted inference for ordered gene expression data. Bioinformatics 2005, 21:3933-3934.
27. Schliep A, Schonhuth A, Steinhoff C: Using hidden Markov models to analyze gene expression time course data. Bioinformatics 2003, 19(Suppl 1):i255-i263.