Glossary of gene expression terms

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See also: gene expression, List of Glossaries, List of Natural Sciences Glossaries

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• A baseline refers to a measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. Baseline expression may also refer to the expected or historical measure of expression for a gene.

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• A constitutive gene or constitutive expression describes a gene that is transcribed continually compared to a facultative gene which is only transcribed as needed.

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• Distance measures are used to measure the dissimilarity between the expressions of different genes".^[1]
  • Down regulation is decreasing the rate of gene expression.

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  • Gene expression is the transcription of DNA into messenger RNA by RNA polymerase. The messenger RNA is then translated into protein by the ribosome.

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  • A facultative gene is a gene which is only transcribed as needed compared to a constitutive gene.

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  • A housekeeping gene is typically a constitutive gene that is transcribed at a relatively constant level across many or all known conditions. The housekeeping gene's products are typically needed for maintenance of the cell. It is generally assumed that their expression is unaffected by experimental conditions. Examples include actin, GAPDH and ubiquitin.

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  • An inducible gene is a gene whose expression is either responsive to environmental change or dependent on the position of the cell cycle.

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  • MAGE stands for MicroArray and Gene Expression, a group that "aims to provide a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems".^[2]
    • MIAMI is a commercial standard developed at MGED based on MAGE to facilitate storage and sharing of gene expression data It stands for Minimum information about a microarray experiment.^[3].
      • MGED is the Microarray Gene Expression Data Society, which "aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments".^[4]

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        • an oligo, short for oligonucleotide is a small chain of nucleic acid residues which are used to detect the presence of larger mRNA molecules. See probe, oligonucleotide array and microarray.

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        • A probe is a term to describe a reagent used to make a single measurement in a gene expression experiment. See reporter, probe-set.
        • A probe-set is a collection of two or more probes that are designed to measure a single molecular species. For example, several oligonucleotides designed to hybrize to various parts of the mRNA generated from a single gene.
        • Promotion is increasing the rate of gene expression.

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        • A reporter is a MIAMI-compliant term to describe a reagent used to make a single measurement in a gene expression experiment. MIAMI defines it as "the nucleotide sequence present in a particular location on the array".^[3] See probe or probe-set.
          • Repression is decreasing the rate of gene expression.

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          • Signature is a vague term which refers to the set of expression measurements which satisfy a certain arbitrary threshold criteria, such as 1.5 fold change with a significance p<0.01. Analysts may define a signature for a given experiment or compare gene signatures across many experiments.
          • Suppression is decreasing the rate of gene expression.

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          • Up regulation is increasing the rate of gene expression.

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          References

          1. ^ Priness, I.; Maimon, O., Ben-Gal, I. (2007). "Evaluation of Gene-Expression Clustering by Mutual Information Distance Measures". BMC Bioinformatics 8 (1): 111. 
          2. ^ A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Tim F. Rayner et al. (2006) BMC Bioinformatics, 7, 489 retrieved 2007-Apr-27
          3. ^ ^{a b} miami1.1 draft 6 retrieved 2007-Apr-27]
          4. ^ http://www.mged.org/ retrieved on 2007-Apr-27