UniPROBE: an online database of protein binding microarray data on protein–DNA interactions

By Daniel E. Newburger, Martha L. Bulyk. Nucleic Acids Res., 2008

405 citations recorded by the source corpus.

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 PBM 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 hosts DNA-binding data for over 175 nonredundant proteins 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. Current web tools 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. The UniPROBE database is available at http://thebrain.bwh.harvard.edu/uniprobe/.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/01e2534187a655b2041d57fe745497c0faf06e6a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning (2016, methodology): “Motifs discovered by DeepCpG were matched to annotated motifs in the Mus musculus CIS-BP [42] and UniPROBE [43] database (version 12.”
Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding (2017, methodology): “…matrix (PWM) models that have been obtained from databases like TRANSFAC (Matys et al. , 2006), Jaspar (Math-69 elier et al. , 2016), UniProbe (Newburger and Bulyk, 2009) or CisBP (Weirauch et al. , 2014), or from motif collections like Factorbook (Wang et al. , 2012), the ENCODE-71 motif…”
An Oncogenic Super-Enhancer Formed Through Somatic Mutation of a Noncoding Intergenic Element (2014, methodology): “(A) All TAL1 enhancer mutations introduce de novo MYB binding sites as determined by UniPROBE (19).”
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity (2014, positive): “, 2013), and data from 674 PBM experiments taken from other studies (compiled in UniPROBE) (Newburger and Bulyk, 2009).”
Annotation of functional variation in personal genomes using RegulomeDB (2012, methodology): “All positional weight matrices from TRANSFAC (Matys et al. 2006), JASPAR CORE (Bryne et al. 2008), and UniPROBE (Berger et al. 2006, 2008; Badis et al. 2009; Newburger and Bulyk 2009; Scharer et al. 2009; Wei etal.”
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites (2015, background): “MotifDb provides access to ScerTF (Spivak and Stormo, 2012), FlyFactorSurvey (Zhu et al. , 2011), hPDI (Xie et al. , 2010), all the selex-generated motifs from (Jolma et al. , 2013), UniPROBE (Newburger and Bulyk, 2009) and JASPAR (Stormo, 2000).”
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data (2019, background): “We collected an extensive set of 4104 positional weight matrices (PWMs) from various online sources [JASPAR (29), HOCOMOCO (30), SwissRegulon (31), UniPROBE (32) and CIS-BP (33)], representing experimentally derived transcription factor binding site motifs of 560 transcription factors (the collectio”
High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions (2010, methodology): “For TFs whose binding domain is not present in the UniPROBE PBM database, we used the most similar binding domain(s) with available PBM data: Pou2f3 and Pou2f1 substituting for Oct4; Sox12 and Sox21 for Sox2; Klf7 for Klf4; and Esrra for Esrrb.”
Transcriptional enhancers: from properties to genome-wide predictions (2014, neutral): “The binding preferences found by different studies are then systematically collected in motif databases such as TRANSFAC 162 , JASPAR 163 and UniPROBE 164 .”
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles (2009, methodology): “The UniPROBE database hosts the PBM datasets and makes the derived matrix profiles available to the community (38).”
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions (2014, methodology): “The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) database (2) was created to provide appropriate curation, easy searching and an informative display interface for universal PBM data.”