Abstract
Mining microarray data to unearth interesting expression profile patterns for discovery of in silico biological knowledge is an emerging area of research in computational biology. A group of functionally related genes may have similar expression patterns under a set of conditions or at some time points. Biclustering is an important data mining tool that has been successfully used to analyze gene expression data for biologically significant cluster discovery. The purpose of this chapter is to introduce interesting patterns that may be observed in expression data and discuss the role of biclustering techniques in detecting interesting functional gene groups with similar expression patterns.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
Notes
References
Kurella M, Hsiao L, Yoshida T, Randall J, Chow G, Sarang S, Jensen R, Gullans S (2001) Dna microarray analysis of complex biologic processes. J Am Soc Nephrol 12:1072–1078
Kraljevic S, Stambrook PJ, Pavelic K (2004) Accelerating drug discovery. EMBO Rep 5:837–842
Yu H, Luscombe N, Qian J, Gerstein M (2003) Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet 19:422–427
Gasch A, Eisen M et al (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3:1–22
Tavazoie S, Hughes J, Campbell M, Cho R, Church G et al (1999) Systematic determination of genetic network architecture. Nat Genet 22:281–285
Grant R (2004) Computational genomics: theory and application. Horizon Bioscience, Cambridge
Li J, Wong L (2001) Emerging patterns and gene expression data. Genome Inform Ser 12:3–13
Alberts B, Johnson A et al (2002) Studying gene expression and function. In: Molecular biology of the cell, 4th edn
Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273–3297
Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6:281–297
Chipman H, Hastie TJ, Tibshirani R (2003) Clustering microarray data. In: Statistical analysis of gene expression microarray data, vol 1. Chapman & Hall/CRC, Boca Raton, pp 159–200
Ahmed HA, Mahanta P, Bhattacharyya D, Kalita JK (2011) Gerc: tree based clustering for gene expression data. In: 2011 I.E. 11th international conference on bioinformatics and bioengineering (BIBE), IEEE, pp 299–302
Mitra S, Banka H (2006) Multi-objective evolutionary biclustering of gene expression data. Pattern Recogn 39:2464–2477
Madeira SC, Oliveira AL (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform 1:24–45
Kriegel HP, Kröger P, Zimek A (2009) Clustering high-dimensional data: a survey on subspace clustering, pattern-based clustering and correlation clustering. ACM Trans Knowl Discov Data (TKDD) 3:1
Mahanta P, Ahmed H, Bhattacharyya D, Kalita JK (2011) Triclustering in gene expression data analysis: a selected survey. In: 2011 2nd national conference on emerging trends and applications in computer science (NCETACS), IEEE pp 1–6
Roy S, Bhattacharyya DK, Kalita JK (2014) Reconstruction of gene co-expression network from microarray data using local expression patterns. BMC Bioinf 15:S10
Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R (2005) Expander—an integrative program suite for microarray data analysis. BMC Bioinf 6:232
Barkow S, Bleuler S, Prelić A, Zimmermann P, Zitzler E (2006) Bicat: a biclustering analysis toolbox. Bioinformatics 22:1282–1283
Gonçalves JP, Madeira SC, Oliveira AL (2009) Biggests: integrated environment for biclustering analysis of time series gene expression data. BMC Res Notes 2:124
Cheng KO, Law NF, Siu WC, Lau T (2007) Bivisu: software tool for bicluster detection and visualization. Bioinformatics 23:2342–2344
Zhou F, Ma Q, Li G, Xu Y (2012) Qserver: a biclustering server for prediction and assessment of co-expressed gene clusters. PloS one 7:e32660
Leung E, Bushel PR (2006) Page: phase-shifted analysis of gene expression. Bioinformatics 22:367–368
Roy S, Bhattacharyya DK, Kalita JK (2013) Cobi: pattern based co-regulated biclustering of gene expression data. Pattern Recogn Lett 34:1669–1678
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodological) 57:289–300
Hartigan JA (1972) Direct clustering of a data matrix. J Am Stat Assoc 67:123–129
Cheng Y, Church G (2000) Biclustering of expression data. In: Proceedings of 8th international conference on intelligent systems for molecular biology, ICISMB’00, vol 8, pp 93–103
Yang J, Wang H, Wang W, Yu P (2003) Enhanced biclustering on expression data. In: Proceedings of the 3rd IEEE symposium on bioinformatics and bioengineering, 2003, pp 321–327
Madeira S, Oliveira A (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinf 1:24–45
Banka H, Mitra S (2006) Evolutionary biclustering of gene expressions. Ubiquity 7:1–12
Aguilar-Ruiz J (2005) Shifting and scaling patterns from gene expression data. Bioinformatics 21:3840–3845
Nepomuceno J, Troncoso A, Aguilar-Ruiz J et al (2011) Biclustering of gene expression data by correlation-based scatter search. BioData Min 4:3
Pei J, Zhang X Cho M, Wang H, Yu P (2003) Maple: a fast algorithm for maximal pattern-based clustering. In: Proceedings of the 3rd IEEE international conference on data mining, 2003 (ICDM’03), IEEE, pp 259–266
Wang H, Chu F, Fan W, Yu P, Pei J (2004) A fast algorithm for subspace clustering by pattern similarity. In: Proceedings of the 16th international conference on scientific and statistical database management, 2004, IEEE, pp 51–60
Tanay A, Sharan R, Shamir R (2002) Discovering statistically significant biclusters in gene expression data. Bioinformatics 18:S136–S144
Roy S, Bhattacharyya DK, Kalita JK (2012) Deterministic approach for biclustering of co-regulated genes from gene expression data. In: Proceedings of the 16th international conference on KES12, FAIA, vol 243, pp 490–499
Eren K, Deveci M, Küçüktunç O, Çatalyürek ÜV (2013) A comparative analysis of biclustering algorithms for gene expression data. Brief Bioinform 14:279–292
Wang H, Wang W, Yang J, Yu P (2002) Clustering by pattern similarity in large data sets. In: Proceedings of the international conference on management of data. ACM SIGMOD’02, ACM, pp 394–405
Zhao Y, Yu J, Wang G, Chen L, Wang B, Yu G (2008) Maximal subspace coregulated gene clustering. IEEE Trans Knowl Data Eng 20:83–98
Prelić A, Bleuler S et al (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 22:1122–1129
Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6:281–297
Ji L, Mock K, Tan K (2006) Quick hierarchical biclustering on microarray gene expression data. In: Proceedings of the 6th IEEE symposium on bioinformatics and bioengineering, 2006 (BIBE’06), IEEE, pp 110–120
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Roy, S., Bhattacharyya, D.K., Kalita, J.K. (2015). Analysis of Gene Expression Patterns Using Biclustering. In: Guzzi, P. (eds) Microarray Data Analysis. Methods in Molecular Biology, vol 1375. Humana Press, New York, NY. https://doi.org/10.1007/7651_2015_280
Download citation
DOI: https://doi.org/10.1007/7651_2015_280
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3172-9
Online ISBN: 978-1-4939-3173-6
eBook Packages: Springer Protocols