JASPAR

JASPAR is an open access and widely used database of

manually curated, non-redundant transcription factor (TF)
JASPAR
binding profiles stored as position frequency matrices
(PFM) and transcription factor flexible models (TFFM)[2] Content
for TFs from species in six taxonomic groups. From the
supplied PFMs, users may generate position-specific Description an open-access
weight matrices (PWM). The JASPAR database was database of transcription
introduced in 2004. There were seven major updates and factor binding profiles
new releases in 2006, 2008, 2010, 2014, 2016, 2018, 2020 Data types Eukaryotic transcription
and 2022, which is the latest release of captured factors, their binding
JASPAR.[3][4][5][6][7][8][9] sites and binding profiles

[10]
Organisms eukaryotes
Contact
Authors Sandelin, A
Primary citation Sandelin, A. et al. (2004)
Availability [1]

Release date 2004

The JASPAR database is an open-source and freely Access
available for scientific community at
http://jaspar.genereg.net/ (http://jaspar.genereg.net/). Website http://jaspar.genereg.net/

Similar databases
TRANSFAC – Transcription Factor Database
HOCOMOCO (http://hocomoco.autosome.ru/) - HOmo sapiens COmprehensive MOdel
COllection
PAZAR (http://www.pazar.info/) - Database with focus on experimentally validated
transcription factor binding sites
TFe (http://www.cisreg.ca/cgi-bin/tfe/home.pl) – the transcription factor encyclopedia
AnimalTFDB – Animal transcription factor database
PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) – 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
TRRD – Transcription Regulatory Regions Database, mainly about regulatory regions and
TF-binding sites
PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) Plant Transcriptional Regulatory Map
MethMotif (https://methmotif.org/) An integrative database of cell-specific transcription factor
binding site motifs coupled with DNA methylation profiles.

References
1. Sandelin, A; Alkema, W; Engström, P; Wasserman, WW; Lenhard, B (1 January 2004).
"JASPAR: an open-access database for eukaryotic transcription factor binding profiles" (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC308747). Nucleic Acids Research. 32 (Database
issue): D91-4. doi:10.1093/nar/gkh012 (https://doi.org/10.1093%2Fnar%2Fgkh012).
PMC 308747 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308747). PMID 14681366 (http
s://pubmed.ncbi.nlm.nih.gov/14681366).
2. Mathelier, A; Wasserman, W.W. (5 September 2013). "The Next Generation of Transcription
Factor Binding Site Prediction" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764009).
PLOS Computational Biology. 9 (9): e1003214. Bibcode:2013PLSCB...9E3214M (https://ui.
adsabs.harvard.edu/abs/2013PLSCB...9E3214M). doi:10.1371/journal.pcbi.1003214 (http
s://doi.org/10.1371%2Fjournal.pcbi.1003214). PMC 3764009 (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC3764009). PMID 24039567 (https://pubmed.ncbi.nlm.nih.gov/24039567).
3. Vlieghe, D; Sandelin, A; De Bleser, PJ; Vleminckx, K; Wasserman, WW; van Roy, F;
Lenhard, B (1 January 2006). "A new generation of JASPAR, the open-access repository for
transcription factor binding site profiles" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC134
7477). Nucleic Acids Research. 34 (Database issue): D95-7. doi:10.1093/nar/gkj115 (https://
doi.org/10.1093%2Fnar%2Fgkj115). PMC 1347477 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC1347477). PMID 16381983 (https://pubmed.ncbi.nlm.nih.gov/16381983).
4. Bryne, JC; Valen, E; Tang, MH; Marstrand, T; Winther, O; da Piedade, I; Krogh, A; Lenhard,
B; Sandelin, A (January 2008). "JASPAR, the open access database of transcription factor-
binding profiles: new content and tools in the 2008 update" (https://www.ncbi.nlm.nih.gov/pm
c/articles/PMC2238834). Nucleic Acids Research. 36 (Database issue): D102-6.
doi:10.1093/nar/gkm955 (https://doi.org/10.1093%2Fnar%2Fgkm955). PMC 2238834 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238834). PMID 18006571 (https://pubmed.ncbi.
nlm.nih.gov/18006571).
5. Portales-Casamar, E; Thongjuea, S; Kwon, AT; Arenillas, D; Zhao, X; Valen, E; Yusuf, D;
Lenhard, B; Wasserman, WW; Sandelin, A (January 2010). "JASPAR 2010: the greatly
expanded open-access database of transcription factor binding profiles" (https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC2808906). Nucleic Acids Research. 38 (Database issue): D105-
10. doi:10.1093/nar/gkp950 (https://doi.org/10.1093%2Fnar%2Fgkp950). PMC 2808906 (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808906). PMID 19906716 (https://pubmed.ncb
i.nlm.nih.gov/19906716).
6. Mathelier, A; Zhao, X; Zhang, AW; Parcy, F; Worsley-Hunt, R; Arenillas, DJ; Buchman, S;
Chen, CY; Chou, A; Ienasescu, H; Lim, J; Shyr, C; Tan, G; Zhou, M; Lenhard, B; Sandelin, A;
Wasserman, WW (January 2014). "JASPAR 2014: an extensively expanded and updated
open-access database of transcription factor binding profiles" (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC3965086). Nucleic Acids Research. 42 (Database issue): D142-7.
doi:10.1093/nar/gkt997 (https://doi.org/10.1093%2Fnar%2Fgkt997). PMC 3965086 (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC3965086). PMID 24194598 (https://pubmed.ncbi.nlm.
nih.gov/24194598).
7. Mathelier, A; Fornes, O; Arenillas, DJ; Chen, CY; Denay, G; Lee, J; Shi, W; Shyr, C; Tan, G;
Worsley-Hunt, R; Zhang, AW; Parcy, F; Lenhard, B; Sandelin, A; Wasserman, WW (4
January 2016). "JASPAR 2016: a major expansion and update of the open-access database
of transcription factor binding profiles" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC47028
42). Nucleic Acids Research. 44 (D1): D110-5. doi:10.1093/nar/gkv1176 (https://doi.org/10.1
093%2Fnar%2Fgkv1176). PMC 4702842 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC47
02842). PMID 26531826 (https://pubmed.ncbi.nlm.nih.gov/26531826).
 8. Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A.;
van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R.; Tan, Ge;
Baranasic, Damir; Arenillas, David J.; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris;
Ballester, Benoît; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony (13 November
2017). "JASPAR 2018: update of the open-access database of transcription factor binding
profiles and its web framework" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753243).
Nucleic Acids Research. 46 (D1): D260–D266. doi:10.1093/nar/gkx1126 (https://doi.org/10.1
093%2Fnar%2Fgkx1126). PMC 5753243 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC57
53243). PMID 29140473 (https://pubmed.ncbi.nlm.nih.gov/29140473).
9. Fornes, Oriol; Castro-Mondragon, Jaime A.; Khan, Aziz; van der Lee, Robin; Zhang, Xi;
Richmond, Phillip A.; Modi, Bhavi P.; Correard, Solenne; Gheorghe, Marius; Baranašić,
Damir; Santana-Garcia, Walter; Tan, Ge; Chèneby, Jeanne; Ballester, Benoit; Parcy,
François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W.; Mathelier, Anthony (8
January 2020). "JASPAR 2020: update of the open-access database of transcription factor
binding profiles" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145627). Nucleic Acids
Research. 48 (D1): D87–D92. doi:10.1093/nar/gkz1001 (https://doi.org/10.1093%2Fnar%2F
gkz1001). PMC 7145627 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145627).
PMID 31701148 (https://pubmed.ncbi.nlm.nih.gov/31701148).
10. Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T (January 2019). "MethMotif: an
integrative cell specific database of transcription factor binding motifs coupled with DNA
methylation profiles" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323897). Nucleic
Acids Research. 47 (D1): D145–D154. doi:10.1093/nar/gky1005 (https://doi.org/10.1093%2
Fnar%2Fgky1005). PMC 6323897 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC632389
7). PMID 30380113 (https://pubmed.ncbi.nlm.nih.gov/30380113).

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