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Multilevel component analysis of time-resolved metabolic fingerprinting data

Jansen, J.J. (author), Hoefsloot, H.C.J. (author), van der Greef, J. (author), Timmerman, M.E. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)

Genomics-based technologies in systems biology have gained a lot of popularity in recent years. These technologies generate large amounts of data. To obtain information from this data, multivariate data analysis methods are required. Many of the datasets generated in genomics are multilevel datasets, in which the variation occurs on different...

article 2005

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In search of secreted protein biomarkers for the anti-inflammatory effect of β2-adrenergic receptor agonists: Application of DIGE technology in combination with multivariate and univariate data analysis tools

Verhoeckx, K.C.M. (author), Gaspari, M. (author), Bijlsma, S. (author), van der Greef, J. (author), Witkamp, R.F. (author), Doornbos, R.P. (author), Rodenburg, R.J.T. (author), TNO Kwaliteit van Leven (author)

Two-dimensional difference gel electrophoresis (DIGE) in combination with univariate (Student's t-test) and multivariate data analysis, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to study the anti-inflammatory effects of the β2-adrenergic receptor (β2-AR) agonist zilpaterol. U937...

article 2005

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Sign constraints improve the detection of differences between complex spectral data sets: LC-IR as an example

Boelens, H.F.M. (author), Eilers, P.H.C. (author), Hankemeier, T. (author), TNO Kwaliteit van Leven (author)

Spectroscopy is a fast and rich analytical tool. On many occasions, spectra are acquired of two or more sets of samples that differ only slightly. These data sets then need to be compared and analyzed, but sometimes it is difficult to find the differences. We present a simple and effective method that detects and extracts new spectral features...

article 2005

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Classification of highly similar crude oils using data sets from comprehensive two-dimensional gas chromatography and multivariate techniques

van Mispelaar, V.G. (author), Smilde, A.K. (author), de Noord, O.E. (author), Blomberg, J. (author), Schoenmakers, P.J. (author), TNO Kwaliteit van Leven (author)

Comprehensive two-dimensional gas chromatography (GC × GC) has proven to be an extremely powerful separation technique for the analysis of complex volatile mixtures. This separation power can be used to discriminate between highly similar samples. In this article we will describe the use of GC × GC for the discrimination of crude oils from...

article 2005

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Expression profiling of colon cancer cell lines and colon biopsies: Towards a screening system for potential cancer-preventive compounds

van Erk, M.J. (author), Krul, C.A.M. (author), Caldenhoven, E. (author), Stierum, R.H. (author), Peters, W.H. (author), Woutersen, R.A. (author), van Ommen, B. (author), TNO Kwaliteit van Leven TNO Voeding (author)

Interest in mechanisms of colon cancer prevention by food compounds is strong and research in this area is often performed with cultured colon cancer cells. In order to assess utility for screening of potential cancer-preventive (food) compounds, expression profiles of 14 human cell lines derived from colonic tissue were measured using cDNA...

article 2005

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Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis

Heijne, W.H.M. (author), Lamers, R.J.A.N. (author), van Bladeren, P.J. (author), Groten, J.P. (author), van Nesselrooij, J.H.J. (author), van Ommen, B. (author), TNO Kwaliteit van Leven (author)

This study investigated whether integrated analysis of transcriptomics and metabolomics data increased the sensitivity of detection and provided new insight in the mechanisms of hepatotoxicity. Metabolite levels in plasma or urine were analyzed in relation to changes in hepatic gene expression in rats that received bromobenzene to induce acute...

article 2005

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Identifying predictors of comfort and discomfort in using hand tools

Kuijt-Evers, L.F.M. (author), Twisk, J. (author), Groenesteijn, L. (author), de Looze, M.P. (author), Vink, P. (author), TNO Kwaliteit van Leven (author)

The aim of the study was to identify predictors of comfort and discomfort in using hand tools. For this purpose, the comfort questionnaire for hand tools (CQH) was developed based on the results of a previous study. In the current study, four screwdrivers were evaluated on comfort (expected comfort at first sight and comfort after short time use...

article 2005

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Integrative Biological Analysis of the APOE*3-Leiden Transgenic Mouse

Clish, C.B. (author), Davidov, E. (author), Oresic, M. (author), Plasterer, T.N. (author), Lavine, G. (author), Londo, T. (author), Meys, M. (author), Snell, P. (author), Stochaj, W. (author), Adourian, A. (author), Zhang, X. (author), Morel, N. (author), Neumann, E. (author), Verheij, E. (author), Vogels, J.T.W.E. (author), Havekes, L.M. (author), Afeyan, N. (author), Regnier, F. (author), van der Greef, J. (author), Naylor, S. (author), TNO Preventie en Gezondheid (author)

Integrative (or systems biology) is a new approach to analyzing biological entities as integrated systems of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. Here, we demonstrate the application of intregrative biological analysis to a mammalian disease model, the apolipoprotein E3-Leiden ...

article 2004

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A combination of proteomics, principal component analysis and transcriptomics is a powerful tool for the identification of biomarkers for macrophage maturation in the U937 cell line

Verhoeckx, K.C.M. (author), Bijlsma, S. (author), de Groene, E.M. (author), Witkamp, R.F. (author), van der Greef, J. (author), Rodenburg, R.J.T. (author), TNO Voeding (author)

The monocyte-like human histiocytic lymphoma cell line U937 can be induced by phorbol 12-myristate 13-acetate (PMA) to undergo differentiation into a macrophage-like phenotype. We have used two-dimensional gel electrophoresis (2-DE), oligonucleotide microarrays and principal component analysis (PCA) to characterize the U937 cell line as a model...

article 2004

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Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model

Davidov, E. (author), Clish, C.B. (author), Oresic, M. (author), Meys, M. (author), Stochaj, W. (author), Snell, P. (author), Lavine, G. (author), Londo, T.R. (author), Adourian, A. (author), Zhang, X. (author), Johnston, M. (author), Morel, N. (author), Marple, E.W. (author), Plasterer, T.N. (author), Neumann, E. (author), Verheij, E. (author), Vogels, J.T.W.E. (author), Havekes, L.M. (author), van der Greef, J. (author), Naylor, S. (author), TNO Preventie en Gezondheid (author)

Multitiered quantitative analysis of biological systems is rapidly becoming the desired approach to study hierarchical functional interactions between proteins and metabolites. We describe here a novel systematic approach to analyze organisms with complex metabolic regulatory networks. By using precise analytical methods to measure biochemical...

article 2004

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Evaluating exposures to complex mixtures of chemicals during a new production process in the plastics industry

Meijster, T. (author), Burstyn, I. (author), van Wendel de Joode, B. (author), Posthumus, M.A. (author), Kromhout, H. (author), TNO Voeding (author)

The goal of this study was to monitor emission of chemicals at a factory where plastics products were fabricated by a new robotic (impregnated tape winding) production process. Stationary and personal air measurements were taken to determine which chemicals were released and at what concentrations. Principal component analyses (PCA) and linear...

article 2004

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Analysis of longitudinal metabolomics data

Jansen, J.J. (author), Hoefsloot, H.C.J. (author), Boelens, H.F.M. (author), van der Greef, J. (author), Smilde, A.K. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)

Motivation: Metabolomics datasets are generally large and complex. Using principal component analysis (PCA), a simplified view of the variation in the data is obtained. The PCA model can be interpreted and the processes underlying the variation in the data can be analysed. In metabolomics, often a priori information is present about the data....

article 2004

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A cardiac-specific health-related quality of life module for young adults with congenital heart disease: Development and validation

Kamphuis, M. (author), Zwinderman, K.A.H. (author), Vogels, T. (author), Vliegen, H.W. (author), Kamphuis, R.P. (author), Ottenkamp, J. (author), Verloove-Vanhorick, S.P. (author), Bruil, J. (author), TNO Preventie en Gezondheid (author)

This study represents the development and validation of a cardiac-specific module of the generic health-related quality of life (HRQoL) instrument, the TAAQOL (TNO/AZL Adult Quality Of Life), for young adults with congenital heart disease (CHD). Items were selected based on literature, an explorative previous study in CHD patients, interviews...

article 2004

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Dietary patterns associated with colon and rectal cancer: Results from the Dietary Patterns and Cancer (DIETSCAN) Project

Dixon, L.B. (author), Balder, H.F. (author), Virtanen, M.J. (author), Rashidkhani, B. (author), Männistö, S. (author), Krogh, V. (author), van den Brandt, P.A. (author), Hartman, A.M. (author), Pietinen, P. (author), Tan, F. (author), Virtamo, J. (author), Wolk, A. (author), Goldbohm, R.A. (author), TNO Voeding (author)

Background: An analysis of dietary patterns or combinations of foods may provide insight regarding the influence of diet on the risk of colon and rectal cancer. Objective: A primary aim of the Dietary Patterns and Cancer (DIETSCAN) Project was to develop and apply a common methodologic approach to study dietary patterns and cancer in 4 European...

article 2004

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Common and Country-Specific Dietary Patterns in Four European Cohort Studies

Balder, H.F. (author), Virtanen, M. (author), Brants, H.A.M. (author), Krogh, V. (author), Dixon, L.B. (author), Tan, F. (author), Mannisto, S. (author), Bellocco, R. (author), Pietinen, P. (author), Wolk, A. (author), Berrino, F. (author), van den Brandt, P.A. (author), Hartman, A.M. (author), Goldbohm, R.A. (author)

The association between diet and cancer, predominantly investigated univariately, has often been inconsistent, possibly because of the large number of candidate risk factors and their high intercorrelations. Analysis of dietary patterns is expected to give more insight than analysis of single nutrients or foods. This study aimed to develop and...

article 2003

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A framework for sequential multiblock component methods

Smilde, A.K. (author), Westerhuis, J.A. (author), de Jong, S. (author), Centraal Instituut voor Voedingsonderzoek TNO TNO Voeding (author)

Multiblock or multiset methods are starting to be used in chemistry and biology to study complex data sets. In chemometrics, sequential multiblock methods are popular; that is, methods that calculate one component at a time and use deflation for finding the next component. In this paper a framework is provided for sequential multiblock methods,...

article 2003

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Changes can be studied when the measurement instrument is different at different time points

Theunissen, N.C.M. (author), Meulman, J.J. (author), den Ouden, L.A. (author), Koopman, H.M. (author), Verrips, E.G.H.W. (author), Verloove-Vanhorick, S.P. (author), Wit, J.M. (author)

article 2003

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Proteome analysis reveals novel proteins associated with proliferation and differentiation of the colorectal cancer cell line Caco-2

Stierum, R. (author), Gaspari, M. (author), Dommels, Y. (author), Ouatas, T. (author), Pluk, H. (author), Jespersen, S. (author), Vogels, J. (author), Verhoeckx, K. (author), Groten, J. (author), van Ommen, B. (author)

Here, we describe a proteomics approach to study protein expression changes in differentiating Caco-2 cells. Caco-2 is a colorectal carcinoma cell line, which upon differentiation loses its tumorigenic phenotype and displays characteristics of mature enterocytes, including brush borders with microvilli. Cells were grown in culture flasks and...

article 2003

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Development and psychometric evaluation of the TAPQOL: A health-related quality of life instrument for 1-5-year-old children

Fekkes, M. (author), Theunissen, N.C.M. (author), Brugman, E. (author), Veen, S. (author), Verrips, E.G.H. (author), Koopman, H.M. (author), Vogels, T. (author), Wit, J.M. (author), Verloove-Vanhorick, S.P. (author)

The 43-item TNO-AZL Preschool Children Quality of Life (TAPQOL) questionnaire was developed to meet the need for a reliable and valid instrument for measuring parent's perceptions of health-related quality of life (HRQoL) in preschool children. HRQoL was defined as health status in 12 domains weighted by the impact of the health status problems...

article 2000