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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...
Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
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SigReannot-mart: a query environment for expression microarray probe re-annotations.

François Moreews1, Gaelle Rauffet, Patrice Dehais

  • 1Sigenae, Institut National de la Recherche Agronomique (INRA), UMR SENAH, 35590 St-Gilles.

Database : the Journal of Biological Databases and Curation
|September 21, 2011
PubMed
Summary

Re-annotating oligonucleotide probes for expression microarrays is crucial as genomic knowledge advances. SigReannot-mart provides updated annotations, aiding researchers in selecting and creating optimal probe sets for transcriptomic studies.

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29:41

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Area of Science:

  • Genomics
  • Bioinformatics
  • Transcriptomics

Background:

  • Expression microarrays utilize oligonucleotide probes to study transcriptomes, with probe design being a time-consuming process often finalized at the project's outset.
  • Over time, advancements in genomic and transcriptomic knowledge necessitate updating probe set annotations to ensure biological relevance and accuracy.

Purpose of the Study:

  • To introduce SigReannot-mart, a query environment for accessing regularly updated annotations for oligonucleotide probe sets.
  • To facilitate the re-annotation of probe sets, particularly for farm and aquaculture species, using the SigReannot pipeline.

Main Methods:

  • The SigReannot pipeline was employed to re-annotate existing oligo sets.
  • SigReannot-mart was populated with these updated annotations, creating a queryable database.
  • The environment allows for filtering and extraction of data in various formats.

Main Results:

  • SigReannot-mart provides a centralized repository of up-to-date annotations for diverse oligo sets.
  • The system enables comparison of probe sets based on multiple criteria.
  • Researchers can utilize SigReannot-mart to select appropriate probe sets for specific experiments or to design novel, combined probe sets.

Conclusions:

  • Regular re-annotation of oligonucleotide probes is essential for maintaining the accuracy and utility of expression microarray data.
  • SigReannot-mart offers a valuable resource for researchers, particularly in agricultural and aquatic genomics, to leverage updated annotations.
  • The tool supports informed decision-making in probe set selection and custom probe set creation for transcriptomic research.