Download PFM data for all taxonomic groups in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for fungi in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Fungi
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for insects in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Insects
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JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for nematodes in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Nematodes
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for plants in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Plants
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for urochordates in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Urochordates
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Download PFM data for vertebrates in JASPAR CORE.
Individual PFMs (zip)
Single batch file (txt)
Vertebrates
JASPAR CORE
The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc.) consist of the open data access, non-redundancy and quality.
When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount
Here you can download XML files for each of the Transcription Factor Flexible Models (TFFMs). For each TFFM there is both a 1st-order and a detailed model each of which is described in a separate XML file.
- TFFM.tar.gz: This tar file contains XML files for each of the Transcription Factor Flexible Models (TFFMs)
- TFFM_table.csv: This file contains additional information about each TFFMs
TFFM_table.csv gives additional information about each TFFM. It contains the following columns:
- TFFM ID - the unique ID of the TFFM including version number
- PFM ID - the JASPAR matrix ID of the profile used initially to train the TFFM
- TF Name - name of the transcription factor
- ChIP-seq file - name of the ChIP-seq peak data file used to train the TFFM
- 1st-order log(p) - log(p-value) of the 1st-order TFFM model
- Detailed log(p) - log(p-value) of the detailed TFFM model
Anthony Mathelier, Wyeth Wasserman, The next generation of transcription factor binding site prediction. PLoS Comput Biol. 2013;9(9):e1003214. doi: 10.1371/journal.pcbi.1003214.
- Sites files: The sequences used to generate the PFM
- BED files: The genomic coordinates of the sequences
- Logos: Sequence logos in SVG format
- Centrality plots: The plots of centrality
Download clustering data for fungi in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Fungi
Download clustering data for insects in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Insects
Download clustering data for nematodes in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Nematodes
Download clustering data for plants in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Plants
Download clustering data for urochordates in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Urochordates
Download clustering data for vertebrates in the CORE and CORE + Unvalidated collections.
CORE + Unvalidated
Vertebrates
- JASPAR2024.sql.gz : SQL dump file
To instantiate an SQLite database from the SQL dump file, use the following command in a Unix shell session:
gunzip -c JASPAR2024.sql.gz | sqlite3 JASPAR2024.sqlite3