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Related Concept Videos

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...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
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Published on: August 5, 2008

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression

Joyce Xiuweu-Xu Gu1, Michael Yang Wei, Pulivarthi H Rao

  • 1Department of Pediatrics, Baylor College of Medicine and Texas Children's Cancer Center, Houston, Texas 77030-2399, USA.

Gene Regulation and Systems Biology
|November 26, 2009
PubMed
Summary
This summary is machine-generated.

Cytogenetics-Genomics Integrator (CGI) is a new Java program that integrates genomic data from different platforms. It correlates DNA copy number changes with RNA expression patterns, aiding biomedical research.

Keywords:
aCGHand data integrationcorrelationexpression profilingvisualization

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Genomic technologies are increasingly used in biomedical research.
  • Integrating data from diverse genomic platforms is crucial for correlating candidate genes and regions.
  • Existing tools lack comprehensive genomic data integration capabilities.

Purpose of the Study:

  • To present a novel Java-based program, Cytogenetics-Genomics Integrator (CGI), for integrating genomic data.
  • To enable correlation of data from array-based comparative genomic hybridization (aCGH) with RNA expression profiling datasets.
  • To provide a user-friendly interface for visualizing and summarizing integrated genomic data.

Main Methods:

  • Developed a Java program (CGI) to match BAC clones from aCGH to genes from RNA expression data.
  • Utilized a MySQL database with UCSC Genome Browser annotations for data matching.
  • Implemented a graphical user interface and Java applet for data visualization and comparison.

Main Results:

  • CGI successfully matches BAC clones to genes, integrating aCGH and gene expression data.
  • The program provides visualization of DNA copy number changes alongside RNA expression patterns.
  • CGI facilitates side-by-side comparison of copy number values and gene expression levels.

Conclusions:

  • CGI offers a valuable tool for integrating and analyzing diverse genomic datasets in biomedical research.
  • The program enhances the correlation of DNA copy number variations with gene expression profiles.
  • CGI is cross-platform compatible, freely available, and designed for biological researchers.