JASPAR

JASPAR
Content
Description an open-access database of transcription factor binding profiles
Data types
captured		 Eukaryotic transcription factors, their binding sites and binding profiles
Organisms eukaryotes
Contact
Authors Sandelin, A
Primary citation Sandelin, A. et al. (2004) [1]
Release date 2004
Access
Website "JASPAR".

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. The JASPAR database was introduced in 2004. There were five major updates and new releases in 2006, 2008, 2010, 2014, 2016 and 2018, which is the latest release of JASPAR.[3][4][5][6][7][8]

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

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". Nucleic Acids Research. 32 (Database issue): D91–4. doi:10.1093/nar/gkh012. PMID 14681366.
  2. ↑ Mathelier, A; Wasserman, W.W. (5 September 2013). "The Next Generation of Transcription Factor Binding Site Prediction". PLoS Computational Biology. 9: e1003214. doi:10.1371/journal.pcbi.1003214. PMID 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". Nucleic Acids Research. 34 (Database issue): D95–7. doi:10.1093/nar/gkj115. PMID 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". Nucleic Acids Research. 36 (Database issue): D102–6. doi:10.1093/nar/gkm955. PMID 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". Nucleic Acids Research. 38 (Database issue): D105–10. doi:10.1093/nar/gkp950. PMID 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". Nucleic Acids Research. 42 (Database issue): D142–7. doi:10.1093/nar/gkt997. PMID 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". Nucleic Acids Research. 44 (D1): D110–5. doi:10.1093/nar/gkv1176. PMID 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". Nucleic Acids Research. doi:10.1093/nar/gkx1126.


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