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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
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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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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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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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Robotics and Dynamic Image Analysis for Studies of Gene Expression in Plant Tissues
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Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.

Guocai Chen1, Juan Camilo Ramírez2, Nan Deng3

  • 1School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.

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We developed ReGEO, a text mining approach to restructure Gene Expression Omnibus (GEO) metadata. This enhances automated reuse of public gene expression data for Big Data research.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Science

Background:

  • Publicly available genomics data, such as from the Gene Expression Omnibus (GEO), is often stored as unstructured text.
  • This unstructured format presents significant challenges for automated data retrieval and analysis.

Purpose of the Study:

  • To develop a method for restructuring and categorizing GEO metadata.
  • To improve the automated reusability and searchability of large-scale public gene expression datasets.

Main Methods:

  • Utilized text mining techniques to analyze GEO metadata.
  • Developed the Restructured GEO database (ReGEO) to reorganize and categorize data.
  • Implemented automated extraction of key experimental attributes (e.g., time points, disease).

Main Results:

  • ReGEO reorganizes GEO series metadata into a structured and searchable format.
  • Introduced new search attributes: number of time points and disease investigated.
  • Enabled searching by existing GEO attributes (organism, experiment type, PubMed ID) and keywords.

Conclusions:

  • The ReGEO approach significantly enhances the usability of GEO data.
  • Demonstrates a viable method for improving the utility of public data in the Big Data era.