UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.
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. The UniPROBE database is available at http://uniprobe.org.
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.
Maxwell A
http://orcid.org/0000-0003-2877-8079
MA
Hume
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
Luis A
LA
Barrera
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Stephen S
SS
Gisselbrecht
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA mlbulyk@receptor.med.harvard.edu.
Martha L
ML
Bulyk
D000465:Algorithms; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D030562:Databases, Protein; D020407:Internet; D059372:Nucleotide Motifs; D040081:Protein Array Analysis; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA