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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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...
What is Gene Expression?01:36

What is Gene Expression?

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 processed and...
What is Gene Expression?01:42

What is Gene Expression?

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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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Published on: October 11, 2019

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

Yao Yu1, Kang Tu, Siyuan Zheng

  • 1Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China. yyu01@sibs.ac.cn

BMC Bioinformatics
|August 26, 2009
PubMed
Summary

GEOGLE is a new tool for gene expression analysis, integrating data from GEO, MeSH, and pathways. It helps researchers quantitatively understand gene expression and phenotypic correlations through meta-analysis.

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Last Updated: Jun 20, 2026

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • High-throughput gene expression technologies generate vast datasets.
  • Traditional data processing pipelines struggle with large-scale biological data.
  • The post-genomic era demands advanced analytical tools.

Purpose of the Study:

  • To develop a context mining tool for gene expression analysis.
  • To facilitate rapid searching of experimental datasets, pathways, and biological terms.
  • To enable quantitative correlation analysis between gene expression and phenotypic distinctions.

Main Methods:

  • Integrated gene expression data from Gene Expression Omnibus (GEO).
  • Utilized biomedical ontology from Medical Subject Headings (MeSH).
  • Incorporated signaling pathway knowledge from sigPathway entries.
  • Developed the GEOGLE context mining tool for comprehensive analysis.

Main Results:

  • GEOGLE enables searching by various queries including GDS IDs, gene IDs, and pathway names.
  • The tool summarizes signature genes from Gene Data Series (GDSes).
  • GEOGLE estimates correlations between gene expression and phenotypic distinctions using integrated p-values.

Conclusions:

  • GEOGLE expands traditional methods for collecting heterogeneous gene expression data.
  • Provides a quantitative approach for understanding gene expression-phenotype correlations.
  • Offers insights into the biological meaning behind gene expression patterns via meta-analysis.