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Related Concept Videos

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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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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Defining diversity, specialization, and gene specificity in transcriptomes through information theory.

Octavio Martínez1, M Humberto Reyes-Valdés

  • 1Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav, Campus Guanajuato, Apartado Postal 629, C.P. 36500 Irapuato, Guanajuato, Mexico. omartine@ira.cinvestav.mx

Proceedings of the National Academy of Sciences of the United States of America
|July 9, 2008
PubMed
Summary

This study introduces a novel framework to quantify transcriptome diversity and gene specificity. These metrics offer a clear understanding of gene expression patterns across tissues and their biological significance.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • The transcriptome, representing all gene transcripts in a tissue, is complex to analyze globally due to thousands of measurements.
  • Existing methods for characterizing transcriptomes face challenges in comprehensively understanding global expression changes.

Purpose of the Study:

  • To develop a quantitative framework for defining and estimating transcriptome diversity and gene specificity.
  • To provide a method for understanding interrelations between transcriptomes and gene expression patterns.

Main Methods:

  • Defined transcriptome diversity using Shannon entropy of gene frequency distributions.
  • Defined gene specificity as mutual information between tissues and transcripts.
  • Introduced formulae and applied them to human tissue gene expression datasets.

Main Results:

  • Developed metrics for transcriptome diversity and gene specificity, distinguishing housekeeping and specific genes.
  • Demonstrated the application of these metrics using human tissue expression data.
  • Visualizations revealed transcriptome interrelations based on diversity and specialization.

Conclusions:

  • The proposed framework offers a powerful way to understand transcriptome diversity and specialization.
  • This approach enhances comprehension of transcriptome dynamics during organism development and in response to stimuli.