Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach

Theoretical Biology and Medical Modelling

Volumn 2, Issue , 2005, Pages

  Boulesteix, Anne Laure ^a   Strimmer, Korbinian ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR; DNA; DNA BINDING PROTEIN;

ALGORITHM; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; PREDICTION; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN INTERACTION; REGRESSION ANALYSIS; SIMULATION; STATISTICAL PARAMETERS; YEAST; BIOLOGICAL MODEL; GENETICS; METABOLISM; MICROARRAY ANALYSIS; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION;

ALGORITHMS; DNA; DNA-BINDING PROTEINS; ESCHERICHIA COLI; LEAST-SQUARES ANALYSIS; MICROARRAY ANALYSIS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION;

EID: 23744491001     PISSN: 17424682     EISSN: None     Source Type: Journal    
DOI: 10.1186/1742-4682-2-23     Document Type: Article

References (33)

1. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP,Young RA: Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
2. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
3. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538.
4. van Steensel B, Delrow J, Bussemaker HJ: Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA-binding. Proc Natl Acad Sci USA 2003, 100:2580-2585.
5. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
6. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifing regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 2003, 34:166-176.
7. Xiong M, Li J, Fang X: Identification of genetic networks. Genetics 2004, 166:1037-1052.
8. Li Z, Chan C: Extracting novel information from gene expression data. Trends Biotechnol 2004, 22:381-383.
9. Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP: Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 2003, 100:15522-15527.
10. Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC: Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci USA 2004, 101:641-646.
11. Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J: RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.Nucleic Acids Res 2001, 29:72-74.
12. Alter O, Golub GH: Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci USA 2004, 101:16577-16582.
13. Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ: Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 2004, 5:R56.
14. Gao F, Foat BC, Bussemaker HJ: Defining transcriptional networks through integrative modeling of mRNA expression and trasncription factor binding data. BMC Bioinformatics 2004, 5:31.
15. Wold S, Martens H, Wold H: The multivariate calibration method in chemistry solved by the PLS method. In Proc. Conf. Matrix Pencils, Lecture Notes in Mathematics Edited by: Ruhe A, Kagstrom B. Heidelberg: Springer Verlag; 1983:286-293.
16. Frank IE, Friedman JH: A statistical view of some chemometrics regression tools. Technometrics 1993, 35:109-135.
17. Martens H: Reliable and relevant modelling of real world data: a personal account of the development of PLS regression. Chemom Intell Lab Syst 2001, 58:85-95.
18. de Jong S: SIMPLS: An alternative approach to partial least squares regression. Chemom Intell Lab Syst 1993, 18:251-253.
19. Braak CJFT, de Jong S: The objective function of partial least squares regression. J Chemometrics 1998, 12:41-54.
20. de Jong S, Wise BM, Ricker NL: Canonical partial least squares and continuum power regression. J Chemometrics 2001, 15:85-100.
21. Datta S: Exploring relationships in gene expressions: a partial least squares approach. Gene Expression 2001, 9:249-255.
22. Nguyen D, Rocke DM: Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 2002, 18:39-50.
23. Nguyen D, Rocke DM: Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics 2002, 18:1625-1632.
24. Boulesteix AL: PLS dimension reduction for classification with microarray data. SAGMB 2004, 3:33.
25. Dudoit S, Fridlyand J, Speed TP: Comparison of discrimination methods for the classification of tumors using gene expression data. J Amer Statist Assoc 2002, 97:77-87.
26. Braga-Neto U, Dougherty ER: Is cross-validation valid for small-sample microarray classification? Bioinformatics 2004, 20:374-380.
27. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
28. 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. Mol Biol Cell 2000, 11:4241-4257.
29. Wichert S, Fokianos K, Strimmer K: Indentifying periodically expressed transcripts in microarray time series data. Bioinformatics 2004, 20:5-20.
30. Buchler NE, Gerland U, Hwa T: On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 2003, 100:5136-5141.
31. Setty Y, Mayo AE, Surette MG, Alon U: Detailed map of a cis-regulatory input function. Proc Natl Acad Sci USA 2003, 100:7702-7707.
32. Yang YL, Suen J, Brynildsen M, Galbraith S, Liao JC: Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 2005, 6:90.
33. R Development Core Team: R: A language and environment for statistical computing. 2004 [http://www.R-project.org]. R Foundation for Statistical Computing, Vienna, Austria [ISBN 3-900051-07-0].