Detecting coherent local patterns from time series gene expression data by a temporal biclustering method

2011 IEEE International Conference on Systems Biology, ISB 2011

Volumn , Issue , 2011, Pages 388-393

  Qu, Ji Bin ^a   Zhang, Xiang Sun ^a   Wu, Ling Yun ^a   Wang, Yong ^a   Chen, Luonan ^b  

^a INSTITUTE OF APPLIED MATHEMATICS   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BICLUSTERING; BICLUSTERS; DISCRETIZATIONS; EXPRESSION PROFILE; LOCAL EXPRESSION; LOCAL PATTERNS; SEQUENCE ALIGNMENTS; TIME DIMENSION; TIME-SERIES GENE EXPRESSION DATA; YEAST CELL CYCLES;

BIOINFORMATICS; DATA REDUCTION; TIME SERIES; TIME SERIES ANALYSIS;

GENE EXPRESSION;

EID: 80054848753     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2011.6033184     Document Type: Conference Paper

References (16)

1. Bar-Joseph Z, Analyzing time series gene expression data, Bioinformatics 2004, 20(16):2493-2503.
2. Androulakis IP, Yang E, Almon RR, Analysis of time-series gene expression data: methods, challenges and opportunities, Annual Review of Biomedical Engineering 2007, 9:205-228.
3. Jiang DX, Tang C, Zhang AD, Cluster analysis for gene expression data: a survey, IEEE Trans. Knowl. Data Eng. 16(11):1370-86. 2004.
4. Prelic A, Bleuler S, Zimmermann P, Wille A, Buhlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E, A systematic comparison and evaluation of biclustering methods for gene expression data, Bioinformatics 2006, 22(10):1282-1283.
5. Madeira SC, Oliveira AL, Biclustering algorithms for biological data analysis: a survey, IEEE/ACM Trans. Comput. Biol. Bioinform., 2004, 1:24-45.
6. Madeira SC, Teixeira MC, S-Correia I, Oliveira AL, Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm, In IEEE/ACM Transactions on Computational Biology and Bioinformatics, 21 Mar. 2008 IEEE Computer Society Digital Library. IEEE Computer Society.
7. Zhang Y, Zha H, Chu CH, A time-series biclustering algorithm for revealing co-Regulated genes, In Proc of the 5th IEEE International Conference on Information Technology: Coding and Computing 2005:32-37.
8. Tanay A, Sharan R, Shamir R, Discovering statistically significant biclusters in gene expression data, Bioinformatics 2002, 18(Suppl 1):S136-S144.
9. Needleman, Saul B, Wunsch, Christian D, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology 48(3):443-53. 1970.
10. Madeira SC, Oliveira AL, An evaluation of discretization methods for non-supervised analysis of time-series gene expression data, Technical Report 42, INESC-ID, December 2005.
11. PT Spellman, G. Sherlock, MQ Zhang, VR Iyer, K Anders, MB Eisen, PO Brown, D Botstein, B Futcher, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Molecular Biology of the Cell, 1998, 9(12):3273-3297.
12. Ji L, Tan K, Identifying time-lagged gene clusters using gene expression data. Bioinformatics 2005, 21(4):509-516.
13. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M, The BioGRID interaction database: 2011 update, Nucleic Acids Res. 2010 Nov. 11.
14. Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sa-Correia I, The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research 2006, 34:D446-D451 [http://www.yeastract.com/ ].
15. J Reimand, M Kull, H Peterson, J Hansen, J Vilo, g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments, NAR 35 W193-W200. 2007
16. 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, Nat. Genet. 2000;25:25-29