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  A new measure for functional similarity of gene products based on Gene Ontology

Schlicker, A., Domingues, F. S., Rahnenführer, J., & Lengauer, T. (2006). A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics, 7, 1-16.

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Datensatz-Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-2206-E Versions-Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-2207-C
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Schlicker_BMCBioinformatics_2006.pdf (beliebiger Volltext), 2MB
 
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Copyright 2006 Schlicker et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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 Urheber:
Schlicker, Andreas1, Autor           
Domingues, Francisco S.1, Autor           
Rahnenführer, Jörg1, Autor           
Lengauer, Thomas1, Autor           
Affiliations:
1Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society, ou_40046              

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 Zusammenfassung: \paragraph*{Background:} Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. \paragraph*{Results:} We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; ${\textit sim_{Rel}}$ and ${\textit funSim}$. One measure (${\textit sim_{Rel}}$) is applied in the comparison of the biological processes found in different groups of organisms. The other measure (${\textit funSim}$) is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. \paragraph*{Conclusions:} The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

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Sprache(n): eng - English
 Datum: 2007-03-132006
 Publikationsstatus: Erschienen
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 Identifikatoren: eDoc: 314476
Anderer: Local-ID: C125673F004B2D7B-BF59AAAC3C285FAEC12571F500572B63-Schlicker_BMCBioinformatics_2006
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Titel: BMC Bioinformatics
Genre der Quelle: Zeitschrift
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Seiten: - Band / Heft: 7 Artikelnummer: - Start- / Endseite: 1 - 16 Identifikator: ISSN: 1471-2105