a comprehensive understanding of gene - expression regulation requires the thorough characterization of transcription factor ( tf)dna binding properties .
tfs play central roles in transcriptional regulatory networks by binding specific dna sequences and activating or repressing gene expression .
dna - binding specificities have broad impact on cell physiology and development and in evolution ( 1,2 ) .
advances in dna microarray synthesis and the development of protein - binding microarray ( pbm ) technology ( 3,4 ) led to the development of universal pbms ( 5 ) , which allow high - throughput measurement of comprehensive data on protein  dna binding specificities , resulting in large data sets requiring curation and searchability .
the universal pbm resource for oligonucleotide - binding evaluation ( uniprobe ) ( 6 ) database was created to satisfy these requirements .
please refer to the original uniprobe publication ( 6 ) for a description of major differences between uniprobe and the jaspar ( 7 ) , transfac ( 8) and pazar ( 9 ) databases .
the original uniprobe publication ( 6 ) also provides a detailed description of pbm technology and data types . since its inception 2 years ago
, the uniprobe database has continued to expand in size , utility and user base .
that number has recently grown to over 400 non - redundant proteins or protein complexes , with additional , unpublished pbm data sets already planned for future deposition . currently , the uniprobe database averages 933 unique visitors per month ( classified by ip address ) from over 40 different countries and 3558 page views per month .
uniprobe is the standard for curating universal pbm data , and we invite other researchers generating universal pbm data to contact us about depositing their data in uniprobe .
uniprobe has more than doubled in size since its introduction in january 2009 ( 6 ) ( table 1 ) . as of this writing , in addition to the data deposited from the initial set of four publications ( 5,1012 ) ,
pbm data are included from six newer publications ( 1318 ) with additional published ( 19 ) and soon to be published data currently in planning for deposition .
the new additions include data on tfs from caenorhabditis elegans , saccharomyces cerevisiae , mus musculus and homo sapiens .
the uniprobe database now houses pbm data for 415 individual proteins or protein complexes , nearly all of which are tfs , corresponding to 404 non - redundant proteins or protein complexes . 

table 1.uniprobe database contents , with indication of additions in pbm data sets since its introduction in 2009referencenumber of proteins or protein complexesspeciesberger et al .
( 18)22mus musculustotal number:415non - redundant proteins or protein complexes:404total , last described ( 6):177total added:238percent increase:134%indicates data sets that have been added since the last published description of uniprobe .
uniprobe database contents , with indication of additions in pbm data sets since its introduction in 2009 indicates data sets that have been added since the last published description of uniprobe .
in the latest version of uniprobe , the available online search features have been augmented with a new search tool that permits a user to perform a blastp ( 20 ) search of a protein sequence of interest ( the  query protein ) against all protein sequences in the uniprobe database ( the  subject proteins ) .
this feature incorporates ncbi s protein  protein blast tool ( 21 ) , blastp v.2.2.23 + , for accurate and efficient alignments .
this blastp tool returns a list of links to the details page for each subject protein that either exactly matches or is similar to the query protein(s ) according to user - specified search parameter settings .
links from the details pages allow further exploration and links to download the pbm data for the matching proteins .
query protein sequences may be entered manually into a web - page form or uploaded as a text file .
multiple sequences can be processed in batch either by specifying one sequence per line , or by entry of fasta - formatted sequences , which may cross multiple lines but are separated by header lines .
numbers and unnecessary white - space are stripped from the sequence prior to performing the search . for the subject proteins ,
the blastp search tool uses a database comprising all the clone insert sequences corresponding to all the pbm experiments with data curated in uniprobe .
for example , consider a search for the human tf gata4 , which is not currently in uniprobe . running the blastp tool on the human gata4 sequence with default parameter settings ( figure 1 ) results in eight hits , four from yeast and four from mouse , all with the gata dna - binding domain ( figure 2 ) . among the hits ,
the tool correctly retrieves two hits to gata3 , which is represented in the database by two proteins : the full - length tf and just the dna - binding domain .
the blastp search parameter settings ( e - value threshold , species , substitution matrix and word size ) are passed directly to a local instance of ncbi s blastp executable . 

figure 1.blastp search of uniprobe with human gata4 protein sequence and default parameter settings for the advanced search options . 

figure 2.results from blastp search of all protein sequences in uniprobe using the human full - length gata4 protein sequence as the query .
blastp search of uniprobe with human gata4 protein sequence and default parameter settings for the advanced search options .
results from blastp search of all protein sequences in uniprobe using the human full - length gata4 protein sequence as the query .
results are output with the sequence matches within matching subject proteins rendered with yellow highlighting on all the residues within the confines of the alignment . also provided is the offset of the first aligned residue of the query protein . as defined by blastp , the score provided is a measure of similarity , and the e - value is the number of expected matches if the subject protein sequences were generated randomly .
each tf pbm data set now has its own uniprobe accession number , regardless of whether or not its protein is unique in the database .
accession numbers are returned as part of the search results and are also listed on each protein s details page .
a user can use the  quick search tool to find tfs by accession number .
accession numbers can be requested prior to publication of new pbm data sets , such as for unpublished pbm data sets in new article submissions .
new to this version of uniprobe is the inclusion of pbm data for protein complexes .
this functionality was implemented to accommodate homodimer and heterodimer data for bhlh tfs from c. elegans ( 13 ) .
this feature allows the details page to render data sets for the protein of interest and for each of the proteins with which the protein of interest dimerizes . the uniprobe statistics cited here were derived with the aid of several minor but useful enhancements .
text search to find tfs by publication ; tfs can be searched by species using the same tool .
to easily distinguish between separate , published pbm data sets for the same protein , a reference to the publication for each separate data set has been added to the bottom of all tf details pages , along with the array design number(s ) . for convenience
a new , shorter url ( http://uniprobe.org ) has been registered , which redirects to the legacy uniprobe url ( http://thebrain.bwh.harvard.edu/uniprobe ) .
future updates planned for uniprobe include additional user and administrative tools . currently in development is a negative control sequence generator which , given an e - score threshold indicative of dna - binding preference , will generate random sequence of user - specified length that does not include any 8-mer with scores exceeding the given threshold for user - selected tfs and species in uniprobe . another planned feature is the display of sequence alignments resulting from the blastp searches of uniprobe . also under development are administrative tools to allow for self - deposition and automated pre - publication uniprobe accession number requests
. the template for the details page will be generalized to support self - deposition of pbm data for protein complexes .
these tools and others will be facilitated , and system performance will generally improve , with the implementation of a newly designed database schema .
as always , we continue to encourage user registration and feedback for error reports and feature requests , some of which motivated the development of the new features described here .
all data hosted by the pbm database are freely available for distribution at the database website . the sequences of the 60-mer dna probes synthesized on the custom - designed universal arrays are available under the terms of the academic research use license available at http://thebrain.bwh.harvard.edu/uniprobe/academic-license.php .
funding for open access charge : national institutes of health ( grant number r01 hg003985 to m.l.b . ) .
 the universal pbm resource for oligonucleotide - binding evaluation ( uniprobe ) database is a centralized repository of information on the dna - binding preferences of proteins as determined by universal protein - binding microarray ( pbm ) technology . 
 each entry for a protein ( or protein complex ) in uniprobe provides the quantitative preferences for all possible nucleotide sequence variants (  words ) of length k (  k - mers ) , as well as position weight matrix ( pwm ) and graphical sequence logo representations of the k - mer data . in this update , 
 we describe > 130% expansion of the database content , incorporation of a protein blast ( blastp ) tool for finding protein sequence matches in uniprobe , the introduction of uniprobe accession numbers and additional database enhancements . 
 the uniprobe database is available at http://uniprobe.org . 
INTRODUCTION
DATABASE ADDITIONS
NEW BLASTP SEARCH FEATURE
UNIPROBE ACCESSION NUMBERS
OTHER NEW FEATURES
FUTURE DIRECTIONS
AVAILABILITY AND LICENSE
FUNDING