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Related Concept Videos

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DNA Microarrays

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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...
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Normal stress is a type of stress that occurs when forces act perpendicular, or normal, to a material's cross-sectional area. This stress often arises in structures when subjected to axial loading, which is the application of force along the axis of an object. A practical example of this can be found in bridge truss members.
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The normal, a continuous distribution, is the most important of all the distributions. Its graph is a bell-shaped symmetrical curve, which is observed in almost all disciplines. Some of these include psychology, business, economics, the sciences, nursing, and, of course, mathematics. Some instructors may use the normal distribution to help determine students’ grades. Most IQ scores are normally distributed. Often real-estate prices fit a normal distribution. The normal distribution is...
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An experiment is a planned activity carried out under controlled conditions. The purpose of an experiment is to investigate the relationship between two variables. When one variable causes change in another, we call the first variable the explanatory or independent variable. The affected variable is called the response or dependent variable. In a randomized experiment, the researcher manipulates values of the explanatory variable and measures the resulting changes in the response variable. The...
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Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
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When a beam is subjected to different loads, such as weight, pressure, or other external forces, internal forces are generated within the beam. These forces can have a significant impact on the overall stability and strength of the structure. Engineers use various methods to analyze and determine the magnitude and direction of these internal forces. One common technique used to determine internal forces in beams is the method of sections. This method involves considering an imaginary point or...
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Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR
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Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling

Thomas Nash1,2, Matthew Huff3, W Bailey Glen1,4

  • 1MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.

Methods in Molecular Biology (Clifton, N.J.)
|January 17, 2019
PubMed
Summary
This summary is machine-generated.

We created a new tool, the Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo), to simplify gene expression analysis in tumor tissues. This R-based pipeline makes complex DNA microarray data analysis more accessible for researchers.

Keywords:
Genomic profilingIllumina Bead arraysMicroarraysNormalizationQuality controlRTumor

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Area of Science:

  • Bioinformatics
  • Genomics
  • Cancer Research

Background:

  • Gene expression analysis is crucial for understanding tumor biology.
  • DNA microarrays are widely used for high-throughput gene expression profiling.
  • Current analysis workflows can be complex and time-consuming.

Purpose of the Study:

  • To introduce PIMENTo, a novel toolkit for streamlining DNA microarray gene expression analysis.
  • To facilitate efficient analysis of gene expression data specifically from tumor tissues.
  • To provide researchers with an accessible R-based solution for complex genomic tasks.

Main Methods:

  • Development of the Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo).
  • Implementation using the R programming language.
  • Integration of open-source packages from CRAN and Bioconductor.

Main Results:

  • PIMENTo simplifies complex gene expression analysis into minimal operations.
  • The toolkit supports comprehensive analysis from data input to quality control.
  • Provides clear documentation on data inputs, outputs, and quality assessment.

Conclusions:

  • PIMENTo offers an efficient and user-friendly approach to DNA microarray analysis.
  • The toolkit empowers researchers to conduct sophisticated gene expression studies with reduced effort.
  • Facilitates reproducible and robust analysis of tumor gene expression data.