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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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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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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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What is Gene Expression?01:42

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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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
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Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis.

Cintia C Palu1,2, Marcelo Ribeiro-Alves3, Yanxin Wu2,4

  • 1School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

Frontiers in Genetics
|May 30, 2019
PubMed
Summary
This summary is machine-generated.

Simplicity DiffExpress empowers wet lab researchers with user-friendly tools for transcriptomics differential expression analysis. This software enhances data exploration and hypothesis validation, improving research reproducibility.

Keywords:
RNA-seqdata-drivendifferential expression analysisdifferential gene expressionedgeRstatistical modelingtranscriptomics

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology

Background:

  • Transcriptomics research generates large datasets requiring complex statistical analysis.
  • Wet lab researchers often lack bioinformatics expertise, hindering data exploration and hypothesis validation.
  • User-friendly interfaces are crucial for enabling non-bioinformaticians to perform robust computational biology analyses.

Purpose of the Study:

  • To provide wet lab researchers with accessible bioinformatics tools for differential expression analysis (DEA).
  • To enhance the exploration of biological data and validation of hypotheses through independent analysis.
  • To improve the quality, reproducibility, and efficiency of transcriptomics research findings.

Main Methods:

  • Development of Simplicity DiffExpress, a data-driven software platform with a user-friendly interface.
  • Integration of edgeR for differential expression analysis.
  • Implementation of bespoke statistical model validation to guide users through data and model adjustments.

Main Results:

  • Simplicity DiffExpress enables non-bioinformaticians to perform DEA independently.
  • The platform offers a dynamic interface with well-organized, navigable, and shareable results.
  • Statistical model validation provides more informative data analysis compared to standard DEA resources.

Conclusions:

  • Simplicity DiffExpress democratizes transcriptomics data analysis for wet lab researchers.
  • The software enhances research independence, data exploration, and hypothesis testing capabilities.
  • It improves the overall quality and reproducibility of findings in transcriptomics studies.