JASPAR
JASPAR provides high-quality, manually curated transcription factor binding profiles as position frequency matrices (PFMs) to model and predict transcription factor binding sites across fungi, insecta, nematoda, plantae, urochordata, and vertebrata for regulatory sequence analysis.
Key Features:
- Curated Profiles: Manually curated, non-redundant transcription factor binding profiles derived from experimentally validated nucleotide sequences ensure high-quality data.
- Position Frequency Matrices (PFMs): Binding profiles are stored as PFMs that can be transformed into predictive models for identifying TF binding sites.
- Taxonomic Coverage: Profiles span six taxonomic groups: fungi, insecta, nematoda, plantae, urochordata, and vertebrata, supporting diverse organismal analyses.
- Matrix Versioning and Updates: Matrices are versioned and updated to refine binding models as new data become available.
- Specialized Collections: Includes collections such as JASPAR FAM (familial TFBS models) and JASPAR phyloFACTS (motifs derived from evolutionarily conserved regulatory regions in mammalian genomes).
- Data Integration: Integrates profiles generated internally via a custom motif discovery pipeline with profiles sourced from external publications and other resources.
- TFBS Enrichment Analysis: Provides an analytical feature for performing transcription factor binding site enrichment analysis in user-supplied genomic regions.
Scientific Applications:
- TFBS Prediction: Predicts transcription factor binding sites in DNA sequences using PFMs converted into predictive models.
- Regulatory Network Analysis: Supports inference and analysis of transcriptional regulatory networks across multiple taxa.
- Promoter and Regulatory Region Analysis: Enables motif-based analysis of promoters and other regulatory regions, including conserved motif detection.
- Comparative and Evolutionary Regulatory Genomics: Facilitates comparative analyses of regulatory motifs and their conservation across species, including mammalian phylogenetic motifs.
- Translational Research: Aids studies of transcriptional control mechanisms relevant to genomics, molecular biology, systems biology, and disease-related research.
Methodology:
Profiles are stored as position frequency matrices (PFMs) and transformed into predictive models; internal profiles are produced by a custom motif discovery pipeline, external profiles are integrated from publications and resources, and specialized collections include motifs derived from evolutionarily conserved regulatory regions; matrix versioning tracks updates.
Topics
Collections
Details
- License:
- CC-BY-4.0
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- Python
- Added:
- 3/18/2015
- Last Updated:
- 8/10/2023
Operations
Data Inputs & Outputs
Publications
Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research. 2019. doi:10.1093/nar/gkz1001. PMID:31701148. PMCID:PMC7145627.
Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Research. 2021;50(D1):D165-D173. doi:10.1093/nar/gkab1113. PMID:34850907. PMCID:PMC8728201.
Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research. 2017;46(D1):D260-D266. doi:10.1093/nar/gkx1126. PMID:29140473. PMCID:PMC5753243.
Khan A, Mathelier A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics. 2017;34(9):1612-1614. doi:10.1093/bioinformatics/btx804. PMID:29253085.
Mathelier A, Fornes O, Arenillas DJ, Chen C, 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. 2015;44(D1):D110-D115. doi:10.1093/nar/gkv1176. PMID:26531826. PMCID:PMC4702842.
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen C, 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. 2013;42(D1):D142-D147. doi:10.1093/nar/gkt997. PMID:24194598. PMCID:PMC3965086.
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. 2009;38(suppl_1):D105-D110. doi:10.1093/nar/gkp950. PMID:19906716. PMCID:PMC2808906.
Bryne JC, Valen E, Tang ME, 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. 2007;36(Database):D102-D106. doi:10.1093/nar/gkm955. PMID:18006571. PMCID:PMC2238834.
Vlieghe D. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Research. 2006;34(90001):D95-D97. doi:10.1093/nar/gkj115. PMID:16381983. PMCID:PMC1347477.
Sandelin A. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research. 2004;32(90001):91D-94. doi:10.1093/nar/gkh012. PMID:14681366. PMCID:PMC308747.
Documentation
Downloads
- API specificationhttps://jaspar.genereg.net/api/
- Downloads pagehttp://jaspar.genereg.net/downloads/
- Source codehttps://github.com/asntech/pyjasparRepository for pyJASPAR