Novel and simple transformation algorithm for combining microarray data sets

Kim, Ki Yeol; Ki, Dong Hyuk; Jeong, Hana; Jeung, Hei Cheul; Chung, Hyun Cheol; Rha, Sun Young

doi:10.1186/1471-2105-8-218

Cited by 10 publications

(4 citation statements)

References 20 publications

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“…Several approaches have been proposed and are generally classified into two main categories: (1) integrate profiles from different studies into one dataset so that available analysis tools can be directly applied to the concatenated dataset or (2) analyze and interpret each dataset separately and subsequently compare the analysis (meta-analysis). 20–27 Since combining data across different platforms remains a serious challenge, meta-analysis approaches are gaining popularity 28,29 given the underlying hypothesis is that even though raw data may not be comparable, the results of the individual analyses are.…”

Section: Introductionmentioning

confidence: 99%

Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing

Acevedo

Berthel

DuBois

et al. 2019

Gene�Regul Syst Bio

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Pharmacological time-series data, from comparative dosing studies, are critical to characterizing drug effects. Reconciling the data from multiple studies is inevitably difficult; multiple in vivo high-throughput -omics studies are necessary to capture the global and temporal effects of the drug, but these experiments, though analogous, differ in (microarray or other) platforms, time-scales, and dosing regimens and thus cannot be directly combined or compared. This investigation addresses this reconciliation issue with a meta-analysis technique aimed at assessing the intrinsic activity at the pathway level. The purpose of this is to characterize the dosing effects of methylprednisolone (MPL), a widely used anti-inflammatory and immunosuppressive corticosteroid (CS), within the liver. A multivariate decomposition approach is applied to analyze acute and chronic MPL dosing in male adrenalectomized rats and characterize the dosing-dependent differences in the dynamic response of MPL-responsive signaling and metabolic pathways. We demonstrate how to deconstruct signaling and metabolic pathways into their constituent pathway activities, activities which are scored for intrinsic pathway activity. Dosing-induced changes in the dynamics of pathway activities are compared using a model-based assessment of pathway dynamics, extending the principles of pharmacokinetics/pharmacodynamics (PKPD) to describe pathway activities. The model-based approach enabled us to hypothesize on the likely emergence (or disappearance) of indirect dosing-dependent regulatory interactions, pointing to likely mechanistic implications of dosing of MPL transcriptional regulation. Both acute and chronic MPL administration induced a strong core of activity within pathway families including the following: lipid metabolism, amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, regulation of essential organelles, and xenobiotic metabolism pathway families. Pathway activities alter between acute and chronic dosing, indicating that MPL response is dosing dependent. Furthermore, because multiple pathway activities are dominant within a single pathway, we observe that pathways cannot be defined by a single response. Instead, pathways are defined by multiple, complex, and temporally related activities corresponding to different subgroups of genes within each pathway.

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Section: Introductionmentioning

confidence: 99%

Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing

Acevedo

Berthel

DuBois

et al. 2019

Gene�Regul Syst Bio

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“…Previous studies have concluded that there were differences between the results from these two types of data sets and the sensitivity to detect differential gene expression from microarray data sets using amplified RNA was also different compared to using total RNA [ 29 , 30 ]. It was also confirmed that systematic biases existed between these two data sets using unsupervised hierarchical cluster analysis [ 31 ].…”

Section: Methodsmentioning

confidence: 67%

Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

Kim

Jeung

et al. 2008

BMC Bioinformatics

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Background: The information from different data sets experimented under different conditions may be inconsistent even though they are performed with the same research objectives. More than that, even when the data sets were generated from the same platform, the data agreement may be affected by the technical variation among the laboratories. In this case, it is necessary to use the combined data set after adjusting the differences between such data sets, for detecting the more reliable information.

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“…By adopting a similar approach to Kim et al [ 36 ] we present a cluster plot in Figure 3 that shows a relationship between the three datasets before data integration. We find that if clustering of individual samples is done using relative gene expressions (i.e expressions of genes in HCV to normal tissue), the samples cluster according to each individual platform, indicating the presence of intra-study variability due to lab/platform effects.…”

Section: Resultsmentioning

confidence: 99%

MAID : An effect size based model for microarray data integration across laboratories and platforms

et al. 2008

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Background: Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of microarray studies has increased, resulting in many different datasets available for any given disease. The increase in sensitivity and reliability of measurements of gene expression changes can be improved through a systematic integration of different microarray datasets that address the same or similar biological questions.

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Novel and simple transformation algorithm for combining microarray data sets

Cited by 10 publications

References 20 publications

Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing

Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing

Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

MAID : An effect size based model for microarray data integration across laboratories and platforms

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