JASPAR is an
open access
Open access (OA) is a set of principles and a range of practices through which nominally copyrightable publications are delivered to readers free of access charges or other barriers. With open access strictly defined (according to the 2001 de ...
and widely used
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
of manually curated, non-redundant
transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
(TF) binding profiles stored as position frequency matrices (PFM) and transcription factor flexible models (TFFM) for TFs from species in six
taxonomic group
In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and ...
s. From the supplied PFMs, users may generate
position-specific weight matrices (PWM). The JASPAR database was introduced in 2004. There were seven major updates and new releases in 2006, 2008, 2010, 2014, 2016, 2018, 2020 and 2022, which is the latest release of JASPAR.
Availability
The JASPAR database is an open-source and freely available for scientific community a
http://jaspar.genereg.net/
Similar databases
*
TRANSFAC – Transcription Factor Database
*
HOCOMOCO - HOmo sapiens COmprehensive MOdel COllection
PAZAR - Database with focus on experimentally validated transcription factor binding sites
TFe – the transcription factor encyclopedia
*
AnimalTFDB – Animal transcription factor database
PlantCARE– cis-regulatory elements and transcription factors in plants (2002)
*
RegTransBase - transcription factor binding sites in a diverse set of bacteria.
*
RegulonDB – Primary database on transcriptional regulation in ''
Escherichia coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
''
* TRRD – Transcription Regulatory Regions Database, mainly about regulatory regions and TF-binding sites
PlantRegMapPlant Transcriptional Regulatory Map
MethMotifAn integrative database of cell-specific transcription factor binding site motifs coupled with DNA methylation profiles.
References
Transcription factors
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