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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...
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Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity
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AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips.

Tancred Frickey1, Vagner Augusto Benedito, Michael Udvardi

  • 1Australian Research Council Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra, Australia.

Plant Physiology
|December 11, 2007
PubMed
Summary
This summary is machine-generated.

Comparing gene expression across species is challenging. AffyTrees is a web tool that identifies orthologous genes on different Affymetrix microarray chips, simplifying cross-species gene expression analysis.

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Published on: April 7, 2011

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microarrays enable simultaneous measurement of large-scale gene expression.
  • Cross-species gene expression comparisons are vital but complicated by the need to identify comparable genes.
  • Existing methods for identifying orthologous genes across different microarray platforms are often labor-intensive.

Purpose of the Study:

  • To develop a user-friendly tool for identifying orthologous genes across various Affymetrix microarray chips.
  • To facilitate accurate cross-species gene expression data comparisons.
  • To aid in improving sequence annotation and detecting biases in microarray chip design.

Main Methods:

  • Implementation of a web-based software tool named AffyTrees.
  • Utilizing phylogenetic trees to determine sequence orthologs.
  • Analysis of probe sets on different Affymetrix chips for orthologous gene identification, even with gene duplications.

Main Results:

  • AffyTrees efficiently assigns probe sets on different Affymetrix chips to orthologous genes.
  • The tool can identify groups of comparable probe sets even when gene or genome duplications are present.
  • Phylogenetic trees generated by AffyTrees serve as a resource for sequence annotation and bias detection.

Conclusions:

  • AffyTrees significantly reduces the workload for cross-species microarray comparisons.
  • Accurate identification of sequence orthologs is crucial for reliable cross-species gene expression analysis.
  • The tool enhances the utility of microarray data for comparative genomics and functional studies.