Welcome to UniPROBE
The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible 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 total, the database currently hosts DNA binding data for 391 nonredundant proteins (individual proteins or in some cases heterodimers) from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human, that have yielded sequence-specific DNA binding site motifs. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. Please click on each tool's "help" link for more information.
News and Updates
- 07/24/09
- New worm PBM data for bHLH domain TFs have been integrated into UniPROBE. These data are described in A multi-parameter network reveals extensive divergence between C. elegans bHLH transcription factors, which has been published in Cell.
- 05/25/09
- Data have been added for the Nsy-7 TF (Caenorhabditis elegans) as described in Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans, and published in Genes and Development.
- 04/14/09
- New mouse PBM data for 104 TFs have been integrated into UniPROBE. These data are described in Diversity and Complexity in DNA Recognition by Transcription Factors, which have been accepted for publication in Science.
- 02/18/09
- Data have been added for the SOX4 TF (homo sapiens) as described in Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer, and published in Cancer Research. Please click here to visit the supplementary materials website for this publication.
- 01/17/09
- Due to an oversight made during the addition of the 89 yeast TFs to UniPROBE, these data were not incorporated into the .zip files in the "All Data" section of the downloads page. The .zip files are now fully up to date, and we apologize for this inconvenience.
- 01/15/09
- New yeast PBM data for 89 TFs have been integrated into UniPROBE. These data are described in High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors, which is in press at Genome Research. Please click here to visit the supplementary materials website for this publication.
- 10/11/08
- A bug in the Search for TF Binding Sites tool has been corrected. Previously, the tool was incorrectly generating the reverse complement of the user entered sequence, which prevented it from finding reverse complement matches. Although the problem did not give rise to any false positive matches, many true positives may have been missed. We apologize for the inconvenience.
- 09/14/08
- The Downloads section now contains zip files holding data for every protein in the database (whereas before the files were segregated by publication), and it also now contains a zip file holding documentation and SQL code for generating many of the database's tables.
- 08/16/08
- The PBM Database has been updated, renamed, and relocated! This current version of the database is now called the UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) Database, and the "Search for Similar Motifs" and "Search for TF Binding Sites" tools are fully implemented.
- 05/16/08
- The PBM database is now public for the mouse homeodomains data! We recommend that you use either Firefox or Internet Explorer for browsing this site. Questions, comments, and suggestions are most welcome at the database help address (
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If you wish to receive PBM Database updates, which will include the addition of new datasets and data analyses, you are encouraged to register for the website here.