UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions

Maxwell A Hume; Luis A Barrera; Stephen S Gisselbrecht; Martha L Bulyk

doi:10.1093/nar/gku1045

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions

Nucleic Acids Res. 2015 Jan;43(Database issue):D117-22. doi: 10.1093/nar/gku1045. Epub 2014 Nov 5.

Authors

Maxwell A Hume¹, Luis A Barrera², Stephen S Gisselbrecht³, Martha L Bulyk⁴

Affiliations

¹ 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.
² 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.
³ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
⁴ 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 [email protected].

Abstract

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
DNA / chemistry
DNA / metabolism
DNA-Binding Proteins / metabolism*
Databases, Protein*
Internet
Nucleotide Motifs
Protein Array Analysis*
Software
Transcription Factors / metabolism*

Substances

DNA-Binding Proteins
Transcription Factors
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding