Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Organelle and Functional Module Resources

Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1053

Synonyms

Definition

An organelle is a discrete structure or specialized subunit within a cell that carries out a specific function. Though originally associated only with eukaryotic cells, recent research has identified similar structures in prokaryotic cells. Organelles are often enclosed within a lipid bilayer membrane and hence are synonymous with “cell compartments” for many cell biologists. However, there are important subunits such as ribosomes which are not membrane-enclosed. The narrowest definition specifies an organelle as a membrane-enclosed and DNA-containing entity (with a particular function): Mitochondria and chloroplasts (in plants) are such examples.

A functional module is the computational equivalent of a (physical) organelle: It is defined as a subunit (typically as a subnetwork in a molecular network) with a specific function. A well-studied example is the chemotaxis functional module of E. coli....

This is a preview of subscription content, log in to check access

References

  1. Cohen-Boulakia S, Froidevaux C, Waller E, Labedan B (2002) Proceedings of JOBIM 2002, Journees Ouvertes, Biologie, Informatique et Mathematiques, Saint-Malou, France, pp 187–193Google Scholar
  2. Hartwell LL, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402(6761 Suppl):C47–C52PubMedGoogle Scholar
  3. Lu Y, Savage LJ, Larson MD, Wilkerson CG, Last RI. (2011) Chloroplast 2010: a database for large-scale phenotype screening of Arabidopsis mutants. Plant Physiol 155(4):1589–1600PubMedGoogle Scholar
  4. Lupi R, de PD Meo, Picardi E, D’Antonio M, Paoletti D, Castrignano T, Pesole G, Gissi C (2010) MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomic studies. Mitochondrion 10:192–199PubMedGoogle Scholar
  5. Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of pedicted functional associations between proteins. Nucleic Acids Res 31(1):258–261Google Scholar
  6. O’Brien EA, Zhang Y, Wang E, Marie V, Badejoko W, Lang BF, Burger G (2009) GOBASE: an organelle genome database. Nucleic Acids Res 37:D946–950PubMedGoogle Scholar
  7. Scott M, Lu G, Hallett M, Thomas DY (2004) The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics 20(6):937–944PubMedGoogle Scholar
  8. Szklarczyk T, Franceschini A, Kuhn M, Simonovic M, Roth A et al (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39:D561–568PubMedGoogle Scholar
  9. Wikipedia (20011) Organelles. http://en.wikipedia.org/wiki/Organelle. Last accessed 2 June 2011

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Computer ScienceUniversity of the Philippines DilimanQuezon CityPhilippines