JASPAR explained

JASPAR
Description:	an open-access database of transcription factor binding profiles
Scope:	Eukaryotic transcription factors, their binding sites and binding profiles
Organism:	eukaryotes
Author:	Sandelin, A
Citation:	Sandelin, A. et al. (2004) ^[1]
Released:	2004
Url:	http://jaspar.genereg.net/

JASPAR is an open access and widely used database of manually curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFM) and transcription factor flexible models (TFFM)^[2] for TFs from species in six taxonomic groups. 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.^{[3] [4] [5] [6] [7] [8] [9] [10]}

Availability

The JASPAR database is an open-source and freely available for scientific community at 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
• TRRD – Transcription Regulatory Regions Database, mainly about regulatory regions and TF-binding sites
• PlantRegMap Plant Transcriptional Regulatory Map
• MethMotif An integrative database of cell-specific transcription factor binding site motifs coupled with DNA methylation profiles.

Notes and References

1. Sandelin. A. Alkema. W. Engström. P. Wasserman. WW. Lenhard. B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles.. Nucleic Acids Research. 1 January 2004. 32. Database issue. D91-4. 10.1093/nar/gkh012. 14681366. 308747.
2. Mathelier. A. Wasserman. W.W.. The Next Generation of Transcription Factor Binding Site Prediction.. PLOS Computational Biology. 5 September 2013. 9. 9. e1003214. 10.1371/journal.pcbi.1003214. 24039567. 3764009. 2013PLSCB...9E3214M. free.
3. Vlieghe. D. Sandelin. A. De Bleser. PJ. Vleminckx. K. Wasserman. WW. van Roy. F. Lenhard. B. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.. Nucleic Acids Research. 1 January 2006. 34. Database issue. D95-7. 10.1093/nar/gkj115. 16381983. 1347477.
4. Bryne. JC. Valen. E. Tang. MH. Marstrand. T. Winther. O. da Piedade. I. Krogh. A. Lenhard. B. Sandelin. A. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.. Nucleic Acids Research. January 2008. 36. Database issue. D102-6. 10.1093/nar/gkm955. 18006571. 2238834.
5. Portales-Casamar. E. Thongjuea. S. Kwon. AT. Arenillas. D. Zhao. X. Valen. E. Yusuf. D. Lenhard. B. Wasserman. WW. Sandelin. A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.. Nucleic Acids Research. January 2010. 38. Database issue. D105-10. 10.1093/nar/gkp950. 19906716. 2808906.
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. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.. Nucleic Acids Research. January 2014. 42. Database issue. D142-7. 10.1093/nar/gkt997. 24194598. 3965086.
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. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.. Nucleic Acids Research. 4 January 2016. 44. D1. D110-5. 10.1093/nar/gkv1176. 26531826. 4702842.
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. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research. 13 November 2017. 10.1093/nar/gkx1126. 46. D1. D260–D266. 29140473. 5753243.
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. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research. 8 January 2020. 10.1093/nar/gkz1001. 48. D1. D87–D92. 31701148. 7145627.
10. Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T . MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles . Nucleic Acids Research . 47 . D1 . D145–D154 . January 2019 . 30380113 . 6323897 . 10.1093/nar/gky1005 . Touati Benoukraf .