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Related Concept Videos

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
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...
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What is Gene Expression?01:36

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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...
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Chromatin Position Affects Gene Expression02:35

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Cell Specific Gene Expression01:58

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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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mRNA Stability and Gene Expression02:51

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The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
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Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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GENT2: an updated gene expression database for normal and tumor tissues.

Seung-Jin Park1,2, Byoung-Ha Yoon1,2, Seon-Kyu Kim3

  • 1Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.

BMC Medical Genomics
|July 13, 2019
PubMed
Summary

The Gene Expression database of Normal and Tumor tissues 2 (GENT2) is an enhanced tool for researchers studying gene expression patterns. It offers expanded tissue data, tumor subtype analysis, and prognostic information for genes.

Keywords:
Cancer subtype profilingLarge scale microarray web-databaseMeta-survival analysisSurvival analysisTissue and cell line wide gene expression profiling

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Area of Science:

  • Bioinformatics
  • Genomics
  • Cancer Research

Background:

  • The Gene Expression database of Normal and Tumor tissues (GENT) provided a platform for exploring gene expression patterns.
  • It compiled gene expression data from public datasets for normal and tumor tissues.

Purpose of the Study:

  • To update and enhance the GENT database with new technologies and expanded functionalities.
  • To provide researchers with a more powerful and user-friendly tool for analyzing gene expression data.

Main Methods:

  • Refactored the database using Apache Lucene indexing for efficient searching.
  • Implemented the Google Web Toolkit (GWT) framework for an improved user interface.
  • Integrated over 68,000 samples, expanding coverage to 72 tissue types.

Main Results:

  • GENT2 now includes gene expression data across 72 tissues, an increase from GENT's 57.
  • New features allow for differential expression analysis based on tumor subtypes and their prognostic significance.
  • Prognostic information and meta-analysis of survival data are provided for genes of interest.

Conclusions:

  • GENT2 represents a significant improvement over its predecessor, offering enhanced capabilities for gene expression analysis.
  • The updated database is expected to remain a valuable resource for a diverse range of scientific researchers.
  • GENT2 is freely accessible online for the research community.