Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

Algorithms for Molecular Biology

Volumn 5, Issue 1, 2010, Pages

  Chia, Burton K H ^a,b   Karuturi, R Krishna Murthy ^b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954311470     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-5-23     Document Type: Article

References (22)

1. Ben-Dor A, Shamir R, Yakhini Z. Clustering gene expression patterns. J Comput Biol 1999, 6(3-4):281-297. 10.1089/106652799318274, 10582567.
2. Dhillon IS, Marcotte EM, Roshan U. Diametrical clustering for identifying anti-correlated gene clusters. Bioinformatics 2003, 19(13):1612-1619. 10.1093/bioinformatics/btg209, 12967956.
3. Golub, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene monitoring. Science 1999, 286:531-537. 10.1126/science.286.5439.531, 10521349.
4. Mirkin B. Mathematical classification and clustering. Nonconvex Optimization and Its Applications 1996, 11. Boston-Dordrecht: Kluwer Academic Publishers, Pardalos PM.
5. Cheng Y, Church GM. Biclustering of expression data. Proceedings of Intl Conf Intell Syst Mol Biol 19-23 August 2000; UC San Diego La Jolla 2000, 93-103. AAAI, Bourne P, Gribskov M, Altman R, Jensen N, Hope D, Lengauer T, Mitchell J, Scheeff E, Smith C, Strande S, Weissig H.
6. Ayadi W, Elloumi M, Hao JK. A biclustering algorithm based on a Bicluster Enumeration Tree: application to DNA microarray data. BioData Mining 2009, 2:9. 10.1186/1756-0381-2-9, 2804695, 20015398.
7. Ihmels J, Bergmann S, Barkai N. Defining transcription modules using large-scale gene expression data. Bioinformatics 2004, 20(13):1993-2003. 10.1093/bioinformatics/bth166, 15044247.
8. Ben-Dor A, Chor B, Karp R, Yakhini Z. Discovering Local Structure in Gene Expression Data: The Order Preserving Submatrix Problem. Jl of Comput Biol 2003, 10(3-4):373-384.
9. Kluger Y, Basri R, Chang JT, Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Research 2003, 13:703-716. 10.1101/gr.648603, 430175, 12671006.
10. Madiera SC, Oliveira AL. Biclustering algorithms for biological data analysis: A survey. IEEE Transactions on Computational Biology and Bioinformatics 2004, 1(1):24-45. 10.1109/TCBB.2004.2, 17048406.
11. Prelic A, Bleuler S, Zimmermann P, Wille A, Bühlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 2006, 22(9):1122-1129. 10.1093/bioinformatics/btl060, 16500941.
12. Tanay A, Sharan R, Shamir R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 2002, 18(1):136-44.
13. Yang J, Wang W, Yu P. Enhanced biclustering on expression data. Proceedings of the 3rd IEEE Conference on Bioinformatics and Bioengineering: 10-12 March 2003 2003, 321-327. Bethesda: IEEE Computer Society.
14. Broët P, Camilleri-Broët S, Zhang S, Alifano M, Bangarusamy D, Battistella M, Wu Y, Tuefferd M, Régnard JF, Lim E, Tan P, Miller LD. Prediction of clinical outcome in multiple lung cancer cohorts by integrative genomics: implications for chemotherapy selection. Cancer Res 2009, 69(3):1055-1062. 10.1158/0008-5472.CAN-08-1116, 19176396.
15. Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IOL, Rijn M, Botstein D, Brown PO. Gene expression patterns in human liver cancers. Mol Biol Cell 2002, 13(6):1929-1939. 10.1091/mbc.02-02-0023., 117615, 12058060.
16. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365(9460):671-679.
17. Kostka D, Spang R. Finding disease specific alterations in the co-expression of genes. Bioinformatics 2004, 20(Suppl 1):i194-i199. 10.1093/bioinformatics/bth909, 15262799.
18. Barkow S, Bleuler S, Prelic A, Zimmermann P, Zitzler E. BicAT: a biclustering analysis toolbox. Bioinformatics 2006, 22(10):1282-1283. 10.1093/bioinformatics/btl099, 16551664.
19. Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Expander: from expression microarrays to networks and functions. Nature Protocols 2010, 5(2):303-322. 10.1038/nprot.2009.230, 20134430.
20. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Molecular Biology of the Cell 2000, 11(12):4241-4257. 15070, 11102521.
21. Alizadeh AA, Eisen MB, Davis ER, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lisheng L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511. 10.1038/35000501, 10676951.
22. Wille A, Zimmermann P, Vranová E, Fürholz A, Laule O, Bleuler S, Hennig L, Prelic A, von Rohr P, Thiele L, Zitzler E, Gruissem W, Bühlmann P. Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biology 2004, 5(11):R92. 10.1186/gb-2004-5-11-r92, 545783, 15535868.