MADMAX – Management and analysis database for multiple ~omics experiments

Lin, Ke; Kools, Harrie J.; Groot, Philip J. de; Gavai, Anand; Basnet, Ram Kumar; Cao, Feng; Wu, Ji; Wang, Xiaowu; Lommen, Arjen; Hooiveld, Guido; Bonnema, Guusje; Visser, Richard G. F.; Müller, Michael; Leunissen, Jack A. M.

doi:10.1515/jib-2011-160

Cited by 120 publications

(61 citation statements)

References 23 publications

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“…The expression data were deposited in the Gene Expression Omnibus (GEO) database (accession number GSE84982). Normalization and analysis of the datasets were performed using MadMax, an in-house, on-line system (Lin et al, 2011). A Variance Stabilization and Normalization (VSN) method was used to obtain expression values.…”

Section: Microarray Hybridization and Data Normalizationmentioning

confidence: 99%

Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

et al. 2016

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The mode of action of silver nanoparticles (AgNPs) is suggested to be exerted through both Ag + and AgNP dependent mechanisms. Ingestion is one of the major NP exposure routes, and potential effects are often studied using Caco-2 cells, a well-established model for the gut epithelium. MCF-7 cells are epithelial breast cancer cells with extensive well-characterized toxicogenomics profiles. In the present study, we aimed to gain a deeper understanding of the cellular molecular responses in Caco-2 and MCF-7 cells after AgNP exposure in order to evaluate whether epithelial cells derived from different tissues demonstrated similar responses. These insights could possibly reduce the size of cell panels for NP hazard identification screening purposes. AgNPs of 20, 30, 60, and 110 nm, and AgNO 3 were exposed for 6 h and 24 h. AgNPs were shown to be taken up and dissolve intracellularly. Compared with MCF-7 cells, Caco-2 cells showed a higher sensitivity to AgNPs, slower gene expression kinetics and absence of NP size-dependent responses. However, on a molecular level, no significant differences were observed between the two cell types. Transcriptomic analysis showed that Ag(NP) exposure caused (oxidative) stress responses, possibly leading to cell death in both cell lines. There was no indication for effects specifically induced by AgNPs. Responses to AgNPs appeared to be induced by silver ions released from the AgNPs. In conclusion, differences in mRNA responses to AgNPs between Caco-2 and MCF-7 cells were mainly related to timing and magnitude, but not to a different underlying mechanism.

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Section: Microarray Hybridization and Data Normalizationmentioning

confidence: 99%

Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

et al. 2016

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“…Intensity based-moderated t-statistics were used to calculate significant differences (18). All data were analyzed using an in-house developed system (19). Data are available in the Gene Expression Omnibus (GEO accession number: GSE61100).…”

Section: Microarray Analysismentioning

confidence: 99%

p21 Ablation in Liver Enhances DNA Damage, Cholestasis, and Carcinogenesis

Ehedego

Boekschoten

et al. 2015

Cancer Research

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Genetic mouse studies suggest that the NF-kB pathway regulator NEMO (also known as IKKg) controls chronic inflammation and carcinogenesis in the liver. However, the molecular mechanisms explaining the function of NEMO are not well defined. Here, we report that overexpression of the cell-cycle regulator p21 is a critical feature of liver inflammation and carcinogenesis caused by the loss of NEMO. NEMO Dhepa mice develop chronic hepatitis characterized by increased hepatocyte apoptosis and proliferation that causes the development of fibrosis and hepatocellular carcinoma (HCC), similar to the situation in human liver disease.

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“…Islam et al, 2016). In brief, expression values of the data were calculated using the robust multichip average (RMA) method and normalised using quantile normalisation in MADMAX Irizarry et al, 2003;Lin et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation

Velpen

Veer

Islam

et al. 2016

Food and Chemical Toxicology

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Quantitative insight into species differences in risk assessment is expected to reduce uncertainty and variability related to extrapolation from animals to humans. This paper explores quantification and comparison of gene expression data between tissues and species from intervention studies with isoflavones.Gene expression data from peripheral blood mononuclear cells (PBMCs) and white adipose tissue (WAT) after 8wk isoflavone interventions in postmenopausal women and ovariectomized F344 rats were used. A multivariate model was applied to quantify gene expression effects, which showed 3 to 5-fold larger effect sizes in rats compared to humans.For estrogen responsive genes, a 5-fold greater effect size was found in rats than in humans.For these genes, intertissue correlations (r=0.23 in humans, r=0.22 in rats) and interspecies correlation in WAT (r=0.31) were statistically significant. Effect sizes, intertissue and interspecies correlations for some groups of genes within energy metabolism, inflammation and cell cycle processes were significant, but weak.Quantification of gene expression data reveals differences between rats and women in effect magnitude after isoflavone supplementation. For risk assessment, quantification of gene expression data and subsequent calculation of intertissue and interspecies correlations within biological pathways will further strengthen knowledge on comparability between tissues and species.

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MADMAX – Management and analysis database for multiple ~omics experiments

Cited by 120 publications

References 23 publications

Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

p21 Ablation in Liver Enhances DNA Damage, Cholestasis, and Carcinogenesis

A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation

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