Query-based biclustering of gene expression data using Probabilistic Relational Models

BMC Bioinformatics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Zhao, Hui ^a   Cloots, Lore ^a   Van den Bulcke, Tim ^b   Wu, Yan ^a   De Smet, Riet ^a   Storms, Valerie ^a   Meysman, Pieter ^a   Engelen, Kristof ^a   Marchal, Kathleen ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b ANTWERP UNIVERSITY HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BI-CLUSTERING; BICLUSTERING ALGORITHM; EXPRESSION PROFILE; FLEXIBLE FRAMEWORK; GENE EXPRESSION DATA; LARGE-SCALE EXPRESSION; PRIOR DISTRIBUTION; PROBABILISTIC RELATIONAL MODELS;

ALGORITHMS; ESCHERICHIA COLI; BIOINFORMATICS;

GENE EXPRESSION;

ESCHERICHIA COLI;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; METHODOLOGY; REGULON; STATISTICAL MODEL;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, GENETIC; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULON;

EID: 79951544186     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S37     Document Type: Article

References (21)

1. Fierro AC, Vandenbussche F, Engelen K, Van de Peer Y, Marchal K. Meta Analysis of Gene Expression Data within and Across Species. Curr Genomics 2008, 9:525-534. 10.2174/138920208786847935, 2694560, 19516959.
2. Owen AB, Stuart J, Mach K, Villeneuve AM, Kim S. A gene recommender algorithm to identify coexpressed genes in C. elegans. Genome Res 2003, 13:1828-1837. 403774, 12902378.
3. Bergmann S, Ihmels J, Barkai N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Res E Stat Nonlin Soft Matter Phys 2003, 67(3 Pt 1):031902.
4. Wu CJ, Kasif S. GEMS: a web server for biclustering analysis of biclustering data. Nucleic Acids Res 2005, 33:W596-W599. 10.1093/nar/gki469, 1160230, 15980544.
5. Dhollander T, Sheng Q, Lemmens K, De Moor B, Marchal K, Moreau Y. Query-driven module discovery in microarray data. Bioinformatics 2007, 23:2573-2580. 10.1093/bioinformatics/btm387, 17686800.
6. Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 2007, 23:2692-2699. 10.1093/bioinformatics/btm403, 17724061.
7. Koller D, Pfeffer A. Probabilistic frame-based systems. Proceedings of the Fifteenth National Conference on Artificial Intelligence: 26-30 July 1998; Madison 1998, 580-587.
8. Friedman N, Getoor L, Koller D, Pfeffer A. Learning probabilistic relational models. International Joint Conference on Artificial Intelligence: 31 July - 6 August 1999; Stockholm 1999, 1300-1309.
9. Getoor L, Friedman N, Koller D, Taskar B. Learning probabilistic models of relational structure. Proceedings of the 18th International Conference on Machine Learning: 2001; San Francisco 2001, 170-177.
10. Madeira SC, Oliveira AL. Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform 2004, 1:24-45. 10.1109/TCBB.2004.2, 17048406.
11. Van den Bulcke T. Robust algorithms for inferring regulatory networks based on gene expression measurements and biological prior information. PhD thesis 2009, Katholieke Universiteit Leuven, Faculty of Engineering.
12. Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society series B 1977, 39:1-38.
13. Prelić 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, 22:1122-1129. 10.1093/bioinformatics/btl060, 16500941.
14. Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, Schoofs G, De Weerdt A, De Moor B, Vanderleyden J, Collado-Vides J, Engelen K, Marchal K. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol 2009, 10:R27. 10.1186/gb-2009-10-3-r27, 2690998, 19265557.
15. Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J. RegulonDB: gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2008, 36:D120-124. 10.1093/nar/gkm994, 2238961, 18158297.
16. ISA matlab package. , http://www2.unil.ch/cbg/index.php?title=ISA
17. QDB source code. , http://homes.esat.kuleuven.be/_tdhollan/Supplementary_Information_Dhollander_2007/index.html
18. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 2009, 37:D464-D470. 10.1093/nar/gkn751, 2686493, 18974181.
19. Frith MC, Fu Y, Yu L, Chen J-F, Hansen U, Weng Z. Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res 2004, 32(4):1372-81. 10.1093/nar/gkh299, 390287, 14988425.
20. NCBI (NC_000913) Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome. , http://www.ncbi.nlm.nih.gov/nuccore/49175990
21. Rivals I, Personnaz L, Taing L, Potier MC. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics 2007, 23:401-407. 10.1093/bioinformatics/btl633, 17182697.