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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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What is Gene Expression?

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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
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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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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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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research.

Hugo López-Fernández1, Aitor Blanco-Míguez2, Florentino Fdez-Riverola3

  • 1ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain; Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Rúa Alfredo Allen, 208, 4200-135, Porto, Portugal.

Computers in Biology and Medicine
|March 9, 2019
PubMed
Summary

DEWE simplifies RNA-Seq analysis for researchers by providing an easy-to-use platform for transcriptomics profiling. This tool streamlines differential gene expression analysis, making complex bioinformatics accessible to all skill levels.

Keywords:
Differential expressionOpen-source softwareRNA-SeqTranslational applicationWorkflow management

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Transcriptomics profiling using RNA-Seq is crucial for understanding gene expression in various biological states.
  • Current RNA-Seq analysis tools often present significant installation and usability challenges for non-bioinformaticians.

Purpose of the Study:

  • To develop a user-friendly platform, DEWE, that simplifies RNA-Seq analysis for both novice and expert users.
  • To provide accessible tools for differential gene expression analysis, quantification, and visualization.

Main Methods:

  • DEWE integrates established workflows using Bowtie2/HISAT2 for alignment and StringTie for quantification.
  • It supports differential expression analysis with Ballgown and edgeR, facilitating tailored execution of individual tools.
  • Docker technology is employed to simplify installation and configuration, reducing user hurdles.

Main Results:

  • DEWE offers an intuitive interface that lowers the learning curve for less experienced users.
  • The platform supports advanced customization and software extension for expert users.
  • High-quality, publication-ready outputs, including figures and pathway enrichment analysis, are generated.

Conclusions:

  • DEWE effectively democratizes RNA-Seq analysis, making complex transcriptomics profiling accessible.
  • The tool's user-friendliness and robust features support diverse research needs, exemplified by a clinical relevance study.
  • DEWE is freely available with comprehensive documentation and installers.