UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.
Bottom Line: The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers').The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos.This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference.
Affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA.Show MeSH
Mentions: Links to the TFBSshape database (33) have been included in the Details pages of proteins with available TFBSshape data. TFBSshape describes the structural features of DNA at TF binding sites, and has entries for proteins corresponding to entries in JASPAR (34,35) and UniPROBE. Figure 4 shows an example of a link and its corresponding TFBSshape web page. Publications with data in UniPROBE whose protein pages currently link to TFBSshape (and vice versa) are: Berger et al., 2006 (1); Berger et al., 2008 (26); Zhu et al., 2009 (27); Badis et al., 2009 (28); Lesch et al., 2009 (30); Scharer et al., 2009 (32). We will continue to correspond with the TFBSshape administrators and provide links for additional publications as they become available in the TFBSshape database.
Affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA.