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

By Maxwell A. Hume, Luis A. Barrera, Stephen S. Gisselbrecht, Martha L. Bulyk. 2014

269 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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1. Richard A. Young
2. Tong Ihn Lee
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Citations in the corpus

• Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, neutral): “The inset is a Venn diagram comparing coverage of mammalian TFs in this work versus in previous large studies using protein-binding microarrays (PBMs) (35, 36) and HT-SELEX (21, 25, 26).”
• Transcription factors activate genes through the phase separation capacity of their activation domains (2018, background): “These DBDs selectively bind specific DNA sequences that range from 4 to 12 bp, and the DNA binding sequences favored by hundreds of TFs have been described (Hume et al., 2015; Jolma et al., 2013; Khan et al., 2018).”
• PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants (2016, methodology): “We firstly collected 1790 binding motifs derived from experiments from multiple databases (including PlantCistromeDB (20), CIS-BP (21), JASPAR (32), UniPROBE (33), TRANSFAC (public 7.0) (34)), literature (22) and motifs discovered from ChIPseq peaks using MEME-ChIP (35).”
• The Human Transcription Factors. (2018, unknown): “…as TRANSFAC (Matys et al., 2006), JASPAR (Mathelier et al., 2016), HT-SELEX (Jolma et al., 2013; Jolma et al., 2015; Yin et al., 2017), UniPROBE (Hume et al., 2015), and CisBP (Weirauch et al., 2014), along with previous catalogs of human TFs (Fulton et al., 2009; Vaquerizas et al., 2009;…”
• PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2015, background): “In recent years, PBM has been widely used in eukaryotic species to evaluate the binding affinity of TFs. UniPROBE, for example, is a database hosting published data generated using PBM technology and covering 22 highly diverse species (11).”
• PEDLA: predicting enhancers with a deep learning-based algorithmic framework (2016, methodology): “We extracted 726 TF motifs from Transfac (52), Jaspar (53) and UniProbe (54) and defined open chromatin in the human genome as the merged TFBS-clustered regions across hundreds of cell types (47), which covers nearly all accessible regions in the human genome.”