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JASPAR

Summary

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]

JASPAR
Content
Descriptionan open-access database of transcription factor binding profiles
Data types
captured		Eukaryotic transcription factors, their binding sites and binding profiles
Organismseukaryotes
Contact
AuthorsSandelin, A
Primary citationSandelin, A. et al. (2004) [1]
Release date2004
Access
Websitehttp://jaspar.genereg.net/
[10]


Availability edit

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

Similar databases edit

  • 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.

References edit

  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. PMC 308747. PMID 14681366.
  2. ^ Mathelier, A; Wasserman, W.W. (5 September 2013). "The Next Generation of Transcription Factor Binding Site Prediction". PLOS Computational Biology. 9 (9): e1003214. Bibcode:2013PLSCB...9E3214M. doi:10.1371/journal.pcbi.1003214. PMC 3764009. 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. PMC 1347477. 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. PMC 2238834. 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. PMC 2808906. 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. PMC 3965086. 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. PMC 4702842. 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. 46 (D1): D260–D266. doi:10.1093/nar/gkx1126. PMC 5753243. PMID 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". Nucleic Acids Research. 48 (D1): D87–D92. doi:10.1093/nar/gkz1001. PMC 7145627. PMID 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". Nucleic Acids Research. 47 (D1): D145–D154. doi:10.1093/nar/gky1005. PMC 6323897. PMID 30380113.