Download JASPAR CORE Position Frequency Matrix (PFM) (non-redundant and redundant) in JASPAR, MEME and TRANSFAC matrix format for six taxonomic groups. More information about matrix formats can be found here.
| Taxonomic group | PFMs (non-redundant) | PFMs (redundant) |
|---|---|---|
| Vertebrates | ||
| Plants | ||
| Insects | ||
| Nematodes | ||
| Fungi | ||
| Urochordates | ||
| All CORE profiles |
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.
The 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
TFFM.tar.gz: This tar file contains XML files for each of the Transcription Factor Flexible Models (TFFMs) (~2 MB)
TFFM_table.csv: This file contains additional information about each TFFMs (~32 KB)
For more detailed documentation about TFFMs please see: http://www.cisreg.ca/TFFM/doc
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.
Download other data including sites, sequence logos, bed files
Sites files: the sequences used to generate the PFM (~66 MB)
BED files: the genomic coordinates of the sequences (~32 MB)
Logos: Sequence logos in SVG format (~90 MB)
Centrality plots: the plots of centrality (~4 MB)
Download JASPAR CORE matrix clustering for five taxonomic groups.
| Taxonomic group | Radial tree [zip] | Clustering summary [zip] |
|---|---|---|
| Vertebrates | ||
| Plants | ||
| Insects | ||
| Nematodes | ||
| Fungi |
Download all the PFMs in JASPAR, MEME and TRANSFAC matrix format for JASPAR collections including CORE, CNE, PHYLO FACTS, SPLICE, POLII, FAM, PBM, PBM HOMEO and PBM HLH.
| Collection | Individual PFMs (zip) | Single batch file (txt) |
|---|---|---|
| CORE |
JASPAR |
MEME |
TRANSFAC (Non-redundant)
JASPAR | MEME | TRANSFAC (Redundant) |
JASPAR |
MEME |
TRANSFAC (Non-redundant)
JASPAR | MEME | TRANSFAC (Redundant) |
| CNE |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| PHYLOFACTS |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| SPLICE |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| POLII |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| FAM |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| PBM |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| PBM_HOMEO |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
| PBM_HLH |
JASPAR | MEME | TRANSFAC | JASPAR | MEME | TRANSFAC |
Download the whole JASPAR 2018 database as mysqldump.