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Related Concept Videos

Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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.
Gene Therapy00:59

Gene Therapy

Gene therapy is a technique where a gene is inserted into a person’s cells to prevent or treat a serious disease. The added gene may be a healthy version of the gene that is mutated in the patient, or it could be a different gene that inactivates or compensates for the patient’s disease-causing gene. For example, in patients with severe combined immunodeficiency (SCID) due to a mutation in the gene for the enzyme adenosine deaminase, a functioning version of the gene can be inserted. The...
Gene Therapy00:59

Gene Therapy

Gene therapy is a technique where a gene is inserted into a person’s cells to prevent or treat a serious disease. The added gene may be a healthy version of the gene that is mutated in the patient, or it could be a different gene that inactivates or compensates for the patient’s disease-causing gene. For example, in patients with severe combined immunodeficiency (SCID) due to a mutation in the gene for the enzyme adenosine deaminase, a functioning version of the gene can be inserted. The...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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Related Experiment Video

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DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
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Novel definition files for human GeneChips based on GeneAnnot.

Francesco Ferrari1, Stefania Bortoluzzi, Alessandro Coppe

  • 1Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100, Modena, Italy. ferrari.francesco@unimore.it

BMC Bioinformatics
|November 17, 2007
PubMed
Summary

New custom Chip Definition Files (CDF) from GeneAnnot ensure accurate gene expression analysis by using unique probesets for single genes, resolving Affymetrix microarray discrepancies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Gene Expression Analysis

Background:

  • Genome annotation improvements revealed issues with Affymetrix microarray probeset/gene assignments.
  • Current Affymetrix human GeneChips often contain probesets matching multiple genes or no transcripts.

Purpose of the Study:

  • To develop novel custom Chip Definition Files (CDF) for Affymetrix human GeneChips.
  • To address discrepancies in gene annotation and probe alignment for accurate gene expression profiling.

Main Methods:

  • Developed custom Chip Definition Files (CDF) using the GeneAnnot database.
  • Created corresponding Bioconductor libraries for Affymetrix human GeneChips.
  • Ensured custom probesets uniquely match single genes.

Main Results:

  • GeneAnnot-based CDFs consist of unique custom probesets, with each probe matching only one gene.
  • Eliminated probesets matching multiple genes, improving data reliability.

Conclusions:

  • GeneAnnot-based custom CDFs enable reliable reconstruction of gene expression levels.
  • Resolved issues of multiple probesets per gene, preventing discordant expression signals.
  • Freely distributed CDF libraries are compliant with Affymetrix standards and analysis software.