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Revision as of 15:52, 17 September 2017
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| 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 binding profiles stored as position frequency matrices (PFM) for TFs across multiple species in six taxonomic groups. JASPAR database was first introduced in 2004 and since then there were five major updates and new releases in 2006, 2008, 2010, 2014 and 2016, which is the latest release of JASPAR.[2][3][4][5][6]
Availability
The JASPAR database is an open-source and freely available for scientific community.
Similar databases
- PlantRegMap - Plant Transcription Factors, cis-elements, binding motifs, and analysis servers
- TRANSFAC – Transcription Factor Database
- AnimalTFDB – Animal transcription factor database
- PLACE – cis-regulatory DNA elements in plants; until February 2007
- PlantCARE – cis-regulatory elements and transcription factors in plants (2002)
- PRODORIC – a similar concept as TRANSFAC for prokaryotes
- RegTransBase - transcription factor binding sites in a diverse set of bacteria.
- RegulonDB – focus on the bacterium Escherichia coli
- SCPD – specific collection of data- and tools for yeast (Saccharomyces cerevisiae) (1998)
- TFe – the transcription factor encyclopedia
- TRRD – Transcription Regulatory Regions Database, mainly about regulatory regions and TF-binding sites
- PAZAR - Database with focus on experimentally validated transcription factor binding sites
- Plant Transcription Factor Database and Transcriptional Regulation Data and Analysis Platform
- HOCOMOCO - Homo Sapiens Comprehensive Model Collection
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.