Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

The prevalence of transpancreatic common hepatic artery and coexisting variant anatomy.

Clinical anatomy (New York, N.Y.)·2017

Same author

Mechanism-based risk assessment strategy for drug-induced cholestasis using the transcriptional benchmark dose derived by toxicogenomics.

The Journal of toxicological sciences·2017

Same author

Association between Volumetric Analysis of Lung Metastases on F-18-fluoro-2-deoxy-D-glucose Positron Emission Tomography/Computed Tomography and Short-term Progression after I-131 Therapy for Differentiated Thyroid Carcinoma.

Indian journal of nuclear medicine : IJNM : the official journal of the Society of Nuclear Medicine, India·2017

Same author

Structural changes in Parkinson's disease: voxel-based morphometry and diffusion tensor imaging analyses based on <sup>123</sup>I-MIBG uptake.

European radiology·2017

Same author

Lumbar plexus in patients with chronic inflammatory demyelinating polyneuropathy: Evaluation with 3D nerve-sheath signal increased with inked rest-tissue rapid acquisition of relaxation enhancement imaging (3D SHINKEI).

European journal of radiology·2017

Same author

Multiparametric voxel-based analyses of standardized uptake values and apparent diffusion coefficients of soft-tissue tumours with a positron emission tomography/magnetic resonance system: Preliminary results.

European radiology·2017

Search research articles

Related Experiment Video

Updated: Sep 2, 2025

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

RAID: Regression Analysis-Based Inductive DNA Microarray for Precise Read-Across.

Yuto Amano¹, Masayuki Yamane¹, Hiroshi Honda¹

¹R&D Safety Science Research, Kao Corporation, Tochigi, Japan.

Frontiers in Pharmacology

|August 8, 2022

Summary

A new virtual DNA microarray, Regression Analysis-based Inductive DNA microarray (RAID), predicts in vivo gene expression from chemical structures and in vitro data. This method refines toxicity assessments and supports animal testing alternatives.

Keywords:

alternative method gene expression analysis hepatotoxicity new approach methodology oligonucleotide array

More Related Videos

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Related Experiment Videos

Last Updated: Sep 2, 2025

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Toxicology
Computational Chemistry
Genomics

Background:

Chemical structure-based read-across is promising for toxicity evaluation but lacks direct in vivo correlation.
In vitro studies for read-across refinement face external validity challenges due to in vitro-in vivo condition gaps.

Purpose of the Study:

To develop a virtual DNA microarray system (RAID) for quantitative prediction of in vivo gene expression profiles.
To enable in vitro to in vivo extrapolation (IVIVE) using chemical structure and in vitro transcriptome data.

Main Methods:

Elastic-net models were built for each gene using chemical descriptors and in vitro transcriptome data to predict in vivo data.
Feature selection identified genes crucial for quantitative structure-activity relationship (QSAR) and IVIVE.
RAID was validated by predicting and analyzing gene expression profiles of hepatotoxic substances.

Main Results:

Predicted transcriptome data from RAID accurately reflected in vivo gene expression profiles of hepatotoxic substances.
Gene ontology and pathway analyses revealed links to nuclear receptor-mediated xenobiotic response and metabolic activation.
Identified IVIVE-related genes were associated with key metabolic pathways, confirming in vitro study effectiveness for these events.

Conclusions:

The RAID system offers a viable alternative screening test for repeated-dose toxicity and toxicogenomics.
RAID provides a critical solution for IVIVE-based read-across by integrating mode of action and chemical structures.
This approach advances non-animal testing methods in chemical safety assessment.