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.
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
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
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
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
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.
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
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
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
JASPAR CNE is a collection of 233 matrix profiles derived by Xie et al.
(PNAS 2007) by clustering of overrepresented motifs from human conserved
non-coding elements. While the biochemical and biological role of most of these
patterns is still unknown, Xie et al. have shown that the most abundant ones
correspond to known DNA-binding proteins, among them is the insulator-binding
protein CTCF.
When should it be used? When characterizing of regulatory inputs in
long-range developmental gene regulation in vertebrates.
The JASPAR FAM database consist of models describing shared binding
properties of structural classes of transcription factors. These types of
models can be called familial profiles, consensus matrices or metamodels. The
models have two prime benefits: 1) Since many factors have similar target
sequences, we often experience multiple predictions at the same locations that
correspond to the same site. This type of models reduce the complexity of the
results. 2) The models can be used to classify newly derived profiles (or
project what type of structural class its cognate transcription factor belongs
to).
When should it be used? When searching large genomic sequences with
no prior knowledge. For classification of new user-supplied profiles.
All the PBM collections are built by using new in-vitro techniques, based on
k-mer microarrays. PBM matrix models have their own database which is
specialized for the data: UniPROBE. The PBM collection is the set derived by
Badis et al (Science 2009) from binding preferences of 104 mouse transcription
factors.
When should it be used? When characterizing of regulatory inputs in
long-range developmental gene regulation in vertebrates.
All the PBM collections are built by using new in-vitro techniques, based on
k-mer microarrays. PBM matrix models have their own database which is
specialized for the data: UniPROBE. The PBM HLH collection is the set derived
by Grove et al (Cell 2008). It holds 19 C. elegans bHLH transcription factor
models.
When should it be used? Where it is important that each matrix was
derived using the same protocol, focusing on bHLH factors.
All the PBM collections are built by using new in-vitro techniques, based on
k-mer microarrays. PBM matrix models have their own database which is
specialized for the data: UniPROBE. The PBM HOMEO collection is the set derived
by Berger et al (Cell 2008) including 176 profiles from mouse homeodomain.
When should it be used? Where it is important that each matrix was
derived using the same protocol, focused on homeobox factors.
The JASPAR PHYLOFACTS database consists of 174 profiles that were extracted
from phylogenetically conserved gene upstream elements. See Xie et al.,
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by
comparison of several mammals., Nature 434, 338-345 (2005) and supplementary
material for details.
When should it be used? The JASPAR PHYLOFACTS matrices are a mix of
known and as of yet undefined motifs. They are useful when one expects that
other factors might determine promoter characteristics, such as structural
aspects and tissue specificity. They are highly complementary to the JASPAR
CORE matrices, so are best used in combination with this matrix set.
The JASPAR POLII database consists of models describing patterns found in
RNA Polymerase II (Pol II) promoters. Some of these correspond to a known
protein (like the TATA box), while some has no specific interactor (like DPE).
Models are taken from published literature or public databases.
When should it be used? When investigating core promoters from
multicellular eukaryotes.
JASPAR SPLICE is a small collection contains matrix profiles of human
canonical and non-canonical splice sites, as matching donor:acceptor pairs. It
currently contains only 6 highly reliable profiles obtained from human genome
made by Chong et al. 2004.
When should it be used? When analyzing splice sites and alternative
splicing.
These profiles are regarded as unvalidated because our curators failed to
find any orthogonal support from existing literature. We encourage the
community to perform experiments and/or point us to literature that our
curators missed in order to support these profiles.
When should it be used? These profiles are not non-validated so we
recommend not to use them.
Download the JASPAR2020 database as SQL dump file.
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