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Related Concept Videos

DNA Microarrays02:34

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...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
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Variability: Analysis

Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
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Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Regulation of Expression Occurs at Multiple Steps

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Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae
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Signal oscillation is another reason for variability in microarray-based gene expression quantification.

Raghvendra Singh1

  • 1Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, India. raghvend@iitk.ac.in

Plos One
|January 26, 2013
PubMed
Summary

Optimizing DNA microarray analysis involves controlling fluid velocity and probe strength. High fluid velocity and strong probes enhance signal and reduce variability, except for SNP detection, which requires weak probes.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Bioinformatics

Background:

  • Microarrays are vital for gene expression, SNP, and disease profiling.
  • Quantification and analysis of microarray data present significant challenges.
  • Previous work linked DNA hybridization rates to target size via diffusion.

Purpose of the Study:

  • To mathematically model transcript surface diffusion on DNA microarrays.
  • To investigate the impact of fluid velocity and probe strength on hybridization dynamics and data quality.
  • To provide recommendations for optimizing microarray experiments.

Main Methods:

  • Mathematical modeling of surface diffusion dynamics.
  • Analysis of hybridization oscillations and signal-to-noise ratios.
  • Simulation of varying fluid velocities and probe strengths.

Main Results:

  • Hybridization dynamics on DNA microarray surfaces are inherently oscillatory.
  • High fluid velocity enhances signal, reduces background, and minimizes oscillation-induced variability.
  • Strong probes decrease inter-microarray variability, while weak probes are optimal for SNP detection.

Conclusions:

  • High fluid velocity and strong probes are recommended for most microarray applications.
  • For SNP detection, high fluid velocity combined with weak probes is advised.
  • Surfaces with high transcript adsorption and desorption rates are beneficial.