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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
Operons02:09

Operons

Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by a repressor...
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...
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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Microarray Analysis for Saccharomyces cerevisiae
13:17

Microarray Analysis for Saccharomyces cerevisiae

Published on: April 7, 2011

Using ontologies to annotate microarray experiments.

Patricia L Whetzel1, Helen Parkinson, Christian J Stoeckert

  • 1Department of Genetics, Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

Methods in Enzymology
|August 31, 2006
PubMed
Summary
This summary is machine-generated.

Consistent annotation of microarray data is crucial for its effective use. The MGED Ontology (MO) provides standardized experimental annotation, supporting the Minimum Information About a Microarray Experiment (MIAME) standard and enhancing data management.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Science

Background:

  • Microarray data management requires consistent annotation for optimal use.
  • Ontologies offer structured terminology essential for scientific data.
  • The Gene Ontology (GO) has improved functional annotation of microarray features.

Purpose of the Study:

  • To introduce the MGED Ontology (MO) for consistent experimental annotation of microarray studies.
  • To support the Minimum Information About a Microarray Experiment (MIAME) standard.
  • To facilitate the integration of experimental metadata into public databases.

Main Methods:

  • Development of the MGED Ontology (MO) as a community effort.
  • Alignment of the MO with the Microarray Gene Expression object model.
  • Incorporation of the MO into existing public microarray database annotation systems.

Main Results:

  • The MGED Ontology (MO) provides a standardized framework for experimental annotation.
  • The MO is freely available and supports the MIAME standard.
  • Several public microarray databases have integrated the MO into their annotation systems.

Conclusions:

  • The MGED Ontology (MO) is a valuable resource for consistent and effective microarray data annotation.
  • Adoption of the MO enhances data comparability and usability across studies.
  • Community-driven development ensures the MO's relevance and applicability in genomics research.