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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Regulation of Expression at Multiple Steps01:23

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.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to 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.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
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Unifying gene expression measures from multiple platforms using factor analysis.

Xin Victoria Wang1, Roel G W Verhaak, Elizabeth Purdom

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America. vwang@jimmy.harvard.edu

Plos One
|March 26, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a unified gene expression measure (UE) using factor analysis (FA) to combine data from multiple microarray platforms in the Cancer Genome Atlas (TCGA) project. The UE provides more accurate and precise expression levels, simplifying downstream analyses.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Cancer Genome Atlas (TCGA) project involves multiple gene expression measurements on the same samples using different microarray platforms.
  • Analyzing data from multiple platforms presents challenges in accuracy, precision, and downstream analysis consolidation.

Purpose of the Study:

  • To develop a method for combining gene expression measurements from multiple microarray platforms.
  • To obtain a more precise and accurate unified gene expression measure (UE).
  • To simplify downstream analyses in the TCGA project.

Main Methods:

  • Factor analysis (FA) was employed to integrate gene expression data from three different microarray platforms.
  • A weighted average approach was used to create the unified gene expression measure (UE).

Main Results:

  • The proposed factor analysis method successfully generated a unified gene expression measure (UE).
  • The UE demonstrated improved accuracy and precision compared to individual platform measurements.
  • The FA model provided parameter estimates for assessing model fit.

Conclusions:

  • Factor analysis is an effective method for creating a unified gene expression measure from multiple platforms.
  • The unified gene expression measure enhances data accuracy and precision for TCGA.
  • This approach simplifies complex multi-platform data analysis in cancer genomics.