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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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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...
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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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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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Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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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.
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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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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mRNA Stability and Gene Expression02:51

mRNA Stability and Gene Expression

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Ribosome Profiling02:24

Ribosome Profiling

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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...
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Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
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Vis-SPLIT: Interactive Hierarchical Modeling for mRNA Expression Classification.

Braden Roper1, James C Mathews2, Saad Nadeem2

  • 1University of Oklahoma.

IEEE Visualization Conference : VIS. IEEE Conference on Visualization
|June 17, 2024
PubMed
Summary
This summary is machine-generated.

Vis-SPLIT is a new visual analytics tool that helps classify patients using gene signatures. It offers better insights into RNA sequencing data for cancer research compared to existing systems.

Keywords:
Human-centered computingVisual analyticsVisualizationVisualization application domains

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate patient classification is crucial for cancer research and treatment.
  • Analyzing complex gene expression data presents significant challenges.

Purpose of the Study:

  • To introduce Vis-SPLIT, an interactive visual analytics tool for partitioning individuals based on gene signatures.
  • To enable users to build cancer classification models by exploring gene expression and correlation data.

Main Methods:

  • Development of Vis-SPLIT, an interactive visual analytics framework.
  • Utilizing visualization components to reveal gene expression and correlation patterns.
  • Interactive exploration and exploitation of visual separations for model building.
  • Case study demonstration and usability evaluation with domain experts.

Main Results:

  • Vis-SPLIT effectively classifies patients based on their genetic signatures.
  • The tool provides valuable insights into RNA sequencing data.
  • Demonstrated superior performance compared to an existing classification system.
  • Usability evaluation confirmed its effectiveness with domain experts.

Conclusions:

  • Vis-SPLIT offers an effective approach for patient classification using gene signatures.
  • The tool enhances the understanding of RNA sequencing data in cancer research.
  • Interactive visualization aids in decision-making for partitioning and classification.