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Related Concept Videos

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.
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...
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Organization of Genes

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Organization of Genes02:07

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General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Published on: June 17, 2012

Ontology annotation: mapping genomic regions to biological function.

Paul D Thomas1, Huaiyu Mi, Suzanna Lewis

  • 1Evolutionary Systems Biology Group, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA. paul.thomas@sri.com

Current Opinion in Chemical Biology
|January 9, 2007
PubMed
Summary

Systems biology requires formal knowledge representation. Ontologies, like the Gene Ontology (GO), map gene functions computationally, integrating literature and evolutionary data for reliable gene annotation.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • The increasing volume of genomic data necessitates a systems approach to biological research.
  • Ontologies offer a formal, computable representation of biological knowledge, crucial for systems biology.
  • Mapping gene function to genomic elements involves ontology building and annotation.

Purpose of the Study:

  • To explore the role of ontologies in systems biology.
  • To discuss two complementary representations of gene function: Gene Ontology (GO) and pathway ontologies.
  • To highlight the process and evidence types in ontology annotation for gene function.

Main Methods:

  • Utilizing ontologies for formal knowledge representation in biology.
  • Employing the Gene Ontology (GO) for gene-centric function representation.
  • Using pathway ontologies to represent biochemical reaction networks.

Main Results:

  • Ontologies provide a computational framework for understanding gene function within biological systems.
  • The Gene Ontology (GO) represents gene function from a gene-centric perspective.
  • Pathway ontologies capture function through biochemical interactions and networks.
  • Ontology annotation integrates scientific literature and evolutionary data to define gene functions.

Conclusions:

  • Ontologies are essential for systems biology, enabling computational analysis of complex biological data.
  • Gene Ontology (GO) and pathway ontologies offer complementary views of gene function.
  • Evidence-based annotation enhances the reliability and utility of ontological representations of gene function.