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Author, Editor

Author(s):

Schlicker, Andreas
Domingues, Francisco S.
Rahnenführer, Jörg
Lengauer, Thomas

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BibTeX cite key*:

Schlicker_BMCBioinformatics_2006

Title

Title*:

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


Schlicker_BMCBioinformatics_2006.pdf (1149.45 KB)

Journal

Journal Title*:

BMC Bioinformatics

Journal's URL:

http://www.biomedcentral.com/bmcbioinformatics

Download URL
for the article:

http://www.biomedcentral.com/content/pdf/1471-2105-7-302.pdf

Language:

English

Publisher

Publisher's
Name:

BioMed Central

Publisher's URL:

http://www.biomedcentral.com/home/

Publisher's
Address:

London, UK

ISSN:

1471-2105

Vol, No, Year, pp.

Volume:

7

Number:


Month:

June

Year*:

2006

Pages:

1-16

Number of VG Pages:


Sequence Number:

302

DOI:


Abstract, Links, (C)

Note:


(LaTeX) Abstract:

\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.

URL for the Abstract:

http://www.biomedcentral.com/1471-2105/7/302

Categories / Keywords:

Bioinformatics, Gene Ontology, Semantic Similarity, Functional Similarity

HyperLinks / References / URLs:


Copyright Message:

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.

Personal Comments:


Download
Access Level:

Public

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Audience:

popular

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort



BibTeX Entry:

@MISC{Schlicker_BMCBioinformatics_2006,
AUTHOR = {Schlicker, Andreas and Domingues, Francisco S. and Rahnenf{\"u}hrer, J{\"o}rg and Lengauer, Thomas},
TITLE = {A new measure for functional similarity of gene products based on {G}ene {O}ntology},
JOURNAL = {BMC Bioinformatics},
PUBLISHER = {BioMed Central},
YEAR = {2006},
VOLUME = {7},
PAGES = {1--16},
ADDRESS = {London, UK},
MONTH = {June},
ISBN = {1471-2105},
}


Entry last modified by Andreas Schlicker, 03/24/2009
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Editor(s)
Andreas Schlicker
Created
09/26/2006 05:52:07 PM
Revisions
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Editor(s)
Andreas Schlicker
Andreas Schlicker
Christine Kiesel
Christine Kiesel
Christine Kiesel
Edit Dates
03/24/2009 06:15:21 PM
13/03/2007 11:28:06
26.02.2007 16:07:44
22.02.2007 14:28:57
29/11/2006 13:42:04
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