Motif databases available for search
The motif databases that can be searched are grouped into 1 category:
Motif Databases
JASPAR CORE
The JASPAR CORE database contains a curated non-redundant set of 123 profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. The prime difference to similar resources (TRANSFAC; TESS etc) consist of the open data access; non-redundancy and quality: JASPAR CORE is a smaller set that is non-redundant and curated.
When should it be used? When seeking models for specific factors or structural classes or if experimental evidence is paramount.
JASPAR PHYLOFACTS
The JASPAR PHYLOFACTS motifs 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-prime 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.
JASPAR FAM
The JASPAR FAM motifs database consist of models describing shared binding properties of structural classes of transcription factors. These types of models can be called familial profiles or consensus matrices or metamodels. The models have two prime benefits: 1) Since many factors have similar tagrget 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.
JASPAR POLII
The JASPAR POLII motifs database consist of models describing patterns found in RNA Polymerase II (Pol II) promoters. Some of these correposnd to a known protein (like the TATA box) while some have 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 CNE
The JASPAR CNE motifs database is a collection of 233 matrix profiles derived 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--most notably insulator-binding protein CTCF.
When should it be used? Characterization of regulatory inputs in long-range developmental gene regulation in vertebrates.
JASPAR SPLICE
The JASPAR SPLICE motifs database 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.
When should it be used? When investigating splice sites.
TRANSFAC
The TRANSFAC transcription factor motifs; contains redundant motifs.
Homeodomains (Berger et al.)
Eukaryotic homeodomain motifs from Berger et al. Cell 133:7 2008 downloaded from http://hugheslab.ccbr.utoronto.ca/supplementary-data/homeodomains1/pwm_all_102107.txt
Yeast (SCPD)
Yeast motifs from the Sacharomyces Cerevisiae Promoter Database downloaded from http://rulai.cshl.edu.
Yeast (MacIsaac v1)
Yeast motifs from computationally derived map (v1.tamo downloaded from http://fraenkel.mit.edu/improved_map).
Drosophila (FLYREG; Bergman & Pollard v2)
Based on FlyReg Drosophila DNase I Footprint Database (v2.0); downloaded from http://www.danielpollard.com/matrices.html.
E. coli (DPINTERACT)
Footprinting databases based on DPINTERACT; downloaded from http://arep.med.harvard.edu/ecoli_matrices.
Prokaryotes (RegTransBase v4)
Manually curated prokaryotic motifs from RegTransBase; downloaded from http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=downloads
Mouse (UNIPROBE)
Mouse TF motifs downloaded from UNIPROBE
Prokaryotes (Prodoric Release 8.9)
Prokaryotic motifs from PRODORIC downloaded from http://prodoric.tu-bs.de/msearch.php.