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Updated: Jun 29, 2026
08:07
Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
Published on: August 2, 2015
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
Daniel E Newburger1, Martha L Bulyk
1Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
Nucleic Acids Research
|October 10, 2008
Summary
The UniPROBE database offers comprehensive in vitro DNA-binding data for over 175 proteins using universal protein binding microarray (PBM) technology. It provides sequence preferences, position weight matrices (PWMs), and tools for motif analysis and binding site identification.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Understanding protein-DNA interactions is crucial for gene regulation.
- Protein binding microarray (PBM) technology enables high-throughput analysis of DNA-binding specificities.
- A centralized resource for PBM data is needed to facilitate research.
Purpose of the Study:
- To establish the UniPROBE database as a centralized repository for universal PBM data.
- To provide access to in vitro DNA-binding specificities for a large set of proteins.
- To offer tools for analyzing protein-DNA binding motifs and identifying binding sites.
Main Methods:
- Collected and curated data from universal protein binding microarray (PBM) experiments.
- Processed PBM data to determine protein sequence preferences for all k-mers.
- Generated position weight matrices (PWMs) and sequence logos from k-mer data.
Main Results:
- The UniPROBE database contains DNA-binding data for over 175 nonredundant proteins from diverse organisms.
- Data includes protein preferences for all sequence variants (k-mers), PWMs, and sequence logos.
- Web tools enable text-based search, motif similarity assessment, and putative binding site identification.
Conclusions:
- UniPROBE serves as a valuable resource for researchers studying protein-DNA interactions.
- The database facilitates the exploration of DNA-binding specificities across various species.
- Integrated web tools enhance the utility of the PBM data for motif discovery and analysis.
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