MPI-INF D3 Publications: Journal Article: A new measure for functional similarity of gene products based on {G}ene {O}ntology

Electronic Journal Article
@Article
Zeitschriftenartikel in einem e-Journal

Show entries of:

this year (2023) | last year (2022) | two years ago (2021) | Notes URL

Action:

Options:

Goto entry point

Author, Editor

Author(s):

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

dblp
dblp
dblp
dblp

BibTeX cite key*:

Schlicker_BMCBioinformatics_2006

Title

Title*:	A new measure for functional similarity of gene products based on Gene Ontology
Attachments:	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

Edit History (please click the blue arrow to see the details)

	Editor(s) Andreas Schlicker	Created 09/26/2006 17:52:07
Revisions 6. 5. 4. 3. 2.	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

Attachment Section

Schlicker_BMCBioinformatics_2006.pdf

Schlicker_BMCBioinformatics_2006.pdf