FunSimMat - Functional Similarity Matrix
FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM
diseases and searching for functional similarity values
for proteins (extracted from UniProt), and protein families (Pfam,
SMART). FunSimMat provides several different semantic and functional similarity measures
for each protein pair using the Gene Ontology annotation
from UniProtKB and the Gene Ontology Annotation project at EBI (GOA).
There are several search options available:
Disease candidate prioritization:
- Rank candidate proteins using any OMIM disease entry
- Compare a list of proteins to any OMIM disease entry
- Compare all human proteins to any OMIM disease entry
Functional similarity:
- Compare one protein / protein family to a list of proteins / protein families
- Compare a list of GO terms to a list of proteins / protein families
Semantic similarity:
- For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values.
Help page
- November 14, 2012: FunSimMat release 6.0 is online.
The current release was built using UniProKB 2012_01, GOA release January 2012, Pfam 26, SMART from InterPro release 35, and OMIM (February 22, 2011).
See the release notes for more details.
- December 17, 2010: FunSimMat release 4.2 is online.
The current release was built using UniProKB 2010_10, GOA release October 2010, Pfam 24, SMART from InterPro release 28, and OMIM (October 12, 2010).
See the release notes for more details.
- September 13, 2010: FunSimMat release 4.1 is online.
The current release was built using UniProKB 2010_08, GOA release July 2010, Pfam 24, SMART from InterPro release 27, and OMIM (July 15, 2010).
See the release notes for more details.
- March 8, 2010: FunSimMat release 4.0 is online.
The current release was built using UniProKB 15.12, GOA release December 2009, Pfam 24, SMART from InterPro release 24, and OMIM
(January 13, 2010).
See the release notes for more details.
- November 18, 2009: A paper describing new features in FunSimMat has been published in Nucleic Acids Research.
You can find it here.
- August 6, 2009: We resolved an issue with the XML-RPC server. If you experience any further problems, please contact us at funsimmat [at] mpi-inf [dot] mpg [dot] de.
We are sorry for any inconveniences caused.
- June 24, 2009: FunSimMat release 3.1 is online.
The current release was built using UniProKB 15.3, GOA release May 2009, Pfam 23, SMART from InterPro release 20, and OMIM (June 10, 2009).
See the release notes for more details.
The query form can be found here.
- Schlicker A., Lengauer T., and Albrecht M.
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
Bioinformatics, 2010, 26(18). doi: 10.1093/bioinformatics/btq384. Paper
- Schlicker A., Albrecht M.
FunSimMat update: new features for exploring functional similarity.
Nucleic Acids Research, 2010, 38(Database issue). doi: 10.1093/nar/gkm979. Paper
- Schlicker A., Albrecht M.
FunSimMat: a comprehensive functional similarity database.
Nucleic Acids Research, 2008, 36(Database issue):D434-439. doi: 10.1093/nar/gkm806. Paper
If you have any questions, comments, suggestions, criticism, or encounter any problem with the web server feel free to contact us at: funsimmat [at] mpi-inf [dot] mpg [dot] de.
