Integrating functional genomics data using maximum likelihood based simultaneous component analysis

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 340-

  van den Berg, Robert A ^a   Van Mechelen, Iven ^a   Wilderjans, Tom F ^a   Van Deun, Katrijn ^a   Kiers, Henk A L ^b   Smilde, Age K ^c  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MECHANISMS; BIOLOGICAL PROCESS; COMPONENT ANALYSIS; CUSTOM-MADE SOLUTIONS; DATA ANALYSIS METHODS; EXPERIMENTAL MODES; FUNCTIONAL GENOMICS; SIMULATION STUDIES;

ESCHERICHIA COLI;

COMPUTER SIMULATION;

ARTICLE; BACTERIAL GENOME; COMPUTER SIMULATION; CONTROLLED STUDY; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; MATHEMATICAL COMPUTING; MAXIMUM LIKELIHOOD METHOD; METABOLOMICS; NONHUMAN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOMICS; LIKELIHOOD FUNCTIONS; METABOLOMICS;

ESCHERICHIA COLI;

EID: 70549098154     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-340     Document Type: Article

References (34)

1. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M. Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations. Science 2007, 316(5824):593-597. 10.1126/science.1132067, 17379776.
2. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 2004, 101(27):10205-10210. 10.1073/pnas.0403218101, 454188, 15199185.
3. Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG. Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. PLoS Comput Biol 2009, 5:e1000270. 10.1371/journal.pcbi.1000270, 2614473, 19180179.
4. Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet 2003, 19(8):422-427. 10.1016/S0168-9525(03)00175-6, 12902159.
5. Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K. Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol 2006, 7(5):R37. 10.1186/gb-2006-7-5-r37, 1779513, 16677396.
6. Kiers HAL, ten Berge JMF. Hierarchical relations between methods for simultaneous component analysis and a technique for rotation to a simple simultaneous structure. Br J Math Stat Psychol 1994, 47:109-126.
7. Timmerman ME, Kiers HAL. Four simultaneous component models for the analysis of multivariate time series from more than one subject to model intraindividual and interindividual differences. Psychometrika 2003, 68:105-121.
8. Bro R, Smilde AK. Centering and scaling in component analysis. J Chemom 2003, 17:16-33.
9. van den Berg RA, Hoefsloot HCJ, Westerhuis JA, Smilde AK, van der Werf MJ. Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 2006, 7:142. 10.1186/1471-2164-7-142, 1534033, 16762068.
10. Van Deun K, Smilde AK, Werf MJ, Kiers HAL, Van Mechelen I. A structured overview of simultaneous component based data integration. BMC Bioinformatics 2009, 10:246. 10.1186/1471-2105-10-246, 2752463, 19671149.
11. Kiers HAL. Towards a standardized notation and terminology in multiway analysis. J Chemom 2000, 14(3):105-122.
12. Smilde AK, Westerhuis JA, de Jong S. A framework for sequential multiblock component methods. J Chemom 2003, 17:323-337.
13. Wilderjans TF, Ceulemans E, Van Mechelen I. Simultaneous analysis of coupled data blocks differing in size: A comparison of two weighting schemes. Comput Stat Data An 2009, 53(4):1086-1098.
14. Carroll J, Chang JJ. Analysis of individual differences in multidimensional scaling via an n-way generalization of 'Eckart-Young' decomposition. Psychometrika 1970, 35(3):283-319.
15. Kroonenberg P, de Leeuw J. Principal component analysis of three-mode data by means of alternating least squares algorithms. Psychometrika 1980, 45:69-97.
16. Kiers HAL, Smilde AK. A comparison of various methods for multivariate regression with highly collinear variables. Stat Methods Appl 2007, 16(2):193-228.
17. Eilers PHC, Boer JM, van Ommen GJ, van Houwelingen HC. Classification of microarray data with penalized logistic regression. Proceedings of SPIE 2001, 4266:187-198. 10.1117/12.427987.
18. Smilde AK, Kiers HAL, Bijlsma S, Rubingh CM, van Erk MJ. Matrix correlations for high-dimensional data: the modified RV-coefficient. Bioinformatics 2009, 25(3):401-405. 10.1093/bioinformatics/btn634, 19073588.
19. van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T. Microbial metabolomics: Toward a platform with full metabolome coverage. Anal Biochem 2007, 370:17-25. 10.1016/j.ab.2007.07.022, 17765195.
20. Smilde AK, van der Werf MJ, Bijlsma S, van der Werff-van der Vat BJC, Jellema RH. Fusion of mass-spectrometry-based metabolomics data. Anal Chem 2005, 77(20):6729-6736. 10.1021/ac051080y, 16223263.
21. van Heijenoort J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat Prod Rep 2001, 18:503-519. 10.1039/a804532a, 11699883.
22. Keseler IM, Vides JC, Castro SG, Ingraham JL, Paley S, Paulsen IT, Gil MP, Karp PD. a comprehensive database resource for Escherichia coli. Nucleic Acids Res 2005, 33(suppl_1):D334-D337. 540062, 15608210.
23. Bos MP, Robert V, Tommassen J. Biogenesis of the gram-negative bacterial outer membrane. Annu Rev Microbiol 2007, 61:191-214. 10.1146/annurev.micro.61.080706.093245, 17506684.
24. Pagès J. Collection and analysis of perceived product inter-distances using multiple factor analysis: Application to the study of 10 white wines from the Loire Valley. Food Qual Pref 2005, 16(7):642-649.
25. de Tayrac M, Le S, Aubry M, Mosser J, Husson F. Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach. BMC Genomics 2009, 10:32. 10.1186/1471-2164-10-32, 2636827, 19154582.
26. Bro R, Sidiropoulos ND, Smilde AK. Maximum likelihood fitting using ordinary least squares algorithms. J Chemom 2002, 16:387-400.
27. Johnston J, DiNardo J. Econometric Methods 1997, New York: McGraw Hill Higher Education, 4, [978-0071259644].
28. Rubingh CM, Bijlsma S, Jellema RH, Overkamp KM, van der Werf MJ, Smilde AK. Analyzing Longitudinal Microbial Metabolomics Data. J Proteome Res 2009, 8(9):4319-4327. 10.1021/pr900126e, 19624157.
29. Blanchard JL, Wholey WY, Conlon EM, Pomposiello PJ. Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks. PLoS ONE 2007, 2(11):e1186. 10.1371/journal.pone.0001186, 2064960, 18000553.
30. Ramsay J, Silverman BW. Functional Data Analysis 2005, New York: Springer, 2, [ISBN-10: 038740080X].
31. Kiers HAL. Weighted least squares fitting using ordinary least squares algorithms. Psychometrika 1997, 62(2):251-266. 10.1007/BF02295279.
32. Gabriel KR, Zamir S. Lower Rank Approximation of Matrices by Least Squares with Any Choice of Weights. Technometrics 1979, 21(4):489-498.
33. Koek M, Muilwijk B, van der Werf MJ, Hankemeier T. Microbial metabolomics with gas chromatography mass spectrometry. Anal Chem 2006, 78(4):1272-1281. 10.1021/ac051683+, 16478122.
34. Coulier L, Bas R, Jespersen S, Verheij E, van der Werf MJ, Hankemeier T. Simultaneous Quantitative Analysis of Metabolites Using Ion-Pair Liquid Chromatography-Electrospray Ionization Mass Spectrometry. Anal Chem 2006, 78(18):6573-6582. 10.1021/ac0607616, 16970336.